Kenya has approximately 57 million people and runs one of the most developed healthcare systems in East Africa. The 2010 constitution devolved health service delivery to 47 county governments, and since then the country has steadily expanded access, digitised health records, and built research infrastructure that holds up against middle-income peers. For organisations working in clinical trial patient recruitment across the continent, Kenya consistently ranks among the top three African countries for trial site density, data maturity, and regulatory capacity.
This profile covers Kenya's health system architecture, disease burden, digital health ecosystem, and research activity. It is written for pharmaceutical companies, CROs, global health funders, and data-focused health organisations assessing the Kenyan market.
Kenya's Health System Structure: National and County Levels
Healthcare governance in Kenya is split between two tiers following the 2013 devolution. The national government, through the Ministry of Health, handles health policy, national referral hospitals, disease surveillance, and regulation. County governments manage primary and secondary health services, including staffing, procurement, and facility management.
The idea behind devolution was to bring decision-making closer to communities and let counties match health spending to local disease patterns. Results have been mixed. Well-resourced counties like Nairobi, Kiambu, Mombasa, and Nakuru have invested heavily in facility upgrades and health worker recruitment. In the arid and semi-arid northern counties (Turkana, Marsabit, Wajir), shortages of both infrastructure and personnel remain severe.
The Kenya Health Policy 2014-2030 sets the strategic direction, with targets for universal health coverage (UHC) that have been tested through pilot programmes in several counties. The Social Health Authority replaced the National Hospital Insurance Fund in 2024 and is now the primary public insurance mechanism. Coverage is still limited: roughly 20 to 30 percent of the population has some form of health insurance.
Healthcare Delivery: Public, Private, and Faith-Based Networks
Health facilities in Kenya are organised into six tiers: community health units at the base, then dispensaries, health centres, sub-county hospitals, county referral hospitals, and national referral hospitals at the top. The two main national referral hospitals are Kenyatta National Hospital (KNH) in Nairobi and Moi Teaching and Referral Hospital (MTRH) in Eldoret, both of which double as academic teaching hospitals linked to the University of Nairobi and Moi University, respectively.
The country has approximately 10,000 to 12,000 registered health facilities. Roughly half are government-owned. The rest are split between private for-profit operators and faith-based organisations. The faith-based sector, coordinated largely through the Kenya Conference of Catholic Bishops (KCCB) and the Christian Health Association of Kenya (CHAK), runs a significant share of rural hospitals and health centres, especially where public facilities are thin on the ground.
Private healthcare is concentrated in urban centres. Nairobi hosts major private hospital groups including Aga Khan University Hospital, Nairobi Hospital, MP Shah Hospital, and expanding chains like Avenue Healthcare and Gertrude's Children's Hospital. These facilities offer higher service standards and shorter wait times, but the costs put them out of reach for most Kenyans without private insurance.
The health workforce remains the biggest constraint across all sectors. Kenya has approximately 20 doctors and 120 nurses per 100,000 population, below WHO recommended thresholds. Distribution is heavily skewed toward Nairobi and other urban centres, leaving many rural counties with ratios well below national averages. Recurring strikes over pay and working conditions have periodically shut down service delivery in the public sector.
Disease Profile and Health Outcomes
Kenya carries a dual burden of communicable and non-communicable diseases, a pattern now common across sub-Saharan Africa. HIV/AIDS, tuberculosis, malaria, and lower respiratory infections remain leading causes of illness and death, though outcomes have improved considerably over the past two decades.
HIV prevalence sits at approximately 3 to 4 percent among adults aged 15 to 49, with roughly 1.4 million people living with HIV. Kenya runs one of Africa's largest antiretroviral therapy (ART) programmes, backed by PEPFAR and the Global Fund. ART coverage has grown substantially, and viral suppression rates continue to improve. Malaria is endemic in the western highlands and coastal lowlands, while Nairobi and the central highlands are largely malaria-free. Tuberculosis, including multi-drug-resistant strains, keeps Kenya on the WHO's high-burden TB country list.
At the same time, non-communicable diseases (NCDs) are rising fast. Cardiovascular disease, diabetes, cancer, and chronic respiratory conditions account for a growing share of hospital admissions and deaths. Adult hypertension prevalence is estimated at 25 to 30 percent, with diabetes prevalence approaching 5 percent in urban areas. Cancer services are thin: the country has only a handful of radiotherapy machines for 57 million people, and oncology referral pathways are fragmented. Co-morbidity profiles are increasingly complex, with clinicians managing patients who have HIV alongside hypertension or diabetes. This makes Kenya relevant to drug development research that requires diverse patient populations.
Maternal and child health indicators have improved but remain poor by global standards. The maternal mortality ratio is estimated at 350 to 500 deaths per 100,000 live births depending on the data source, and under-five mortality still exceeds 40 per 1,000 live births in several counties. These numbers reflect the uneven nature of Kenya's health transition and the need for county-level data disaggregation in planning.
Digital Health Leadership: OpenMRS, M-Pesa Health, and Beyond
Kenya is one of Africa's strongest performers in digital health. Nairobi's position as a continental tech hub has produced real innovations in mobile health, electronic medical records, and health information exchange that other African countries now look to as reference points.
The backbone of Kenya's health data system is the District Health Information Software 2 (DHIS2), which is the national health management information system. Deployed across all 47 counties, DHIS2 aggregates routine health facility data and gives the Ministry of Health the epidemiological surveillance it needs for planning and resource allocation.
At the facility level, Kenya has one of the most extensive EMR deployments in sub-Saharan Africa. OpenMRS, the open-source medical records system developed through a collaboration between Regenstrief Institute and Partners In Health, runs in more than 2,300 health facilities across the country, many of them PEPFAR-supported sites. KenyaEMR, a nationally customised distribution of OpenMRS, is the standard system for HIV care and treatment documentation and has been gradually expanded to cover general outpatient and maternal health services.
Other EMR systems also operate in Kenya. IQCare was historically used for HIV programme management. Funsoft and other proprietary systems serve parts of the private sector. The main problem is interoperability: these systems have historically operated as isolated data silos, which is also where the biggest opportunity lies.
Mobile health has taken off in Kenya partly because M-Pesa normalised digital transactions and created a platform that health services could build on. M-TIBA, a mobile health wallet linked to M-Pesa, lets users save, send, and spend funds earmarked specifically for healthcare. Other mobile platforms support community health worker data collection, appointment reminders, and medication adherence tracking. With mobile money accounts reaching the vast majority of adult Kenyans, the country has distribution channels for health interventions that few other African markets can match.
Health Data Infrastructure and Interoperability
Kenya's health data environment is characterised by breadth of deployment and a growing but incomplete push toward interoperability. The Kenya Health Information System Policy and the Kenya Standards and Guidelines for E-Health provide the regulatory scaffolding for health data management, mandating the use of standard coding systems and data exchange protocols across public health facilities.
In practice, interoperability remains a work in progress. The Health Information Mediator, based on the OpenHIE architecture, has been piloted as a national health information exchange (HIE) layer to enable data sharing between EMR systems, the national laboratory information system, and DHIS2. The Interoperability Layer (IL) connects KenyaEMR instances to the national data warehouse, enabling aggregate reporting while maintaining patient-level records at facility level.
ICD-10 coding is increasingly standard for diagnosis classification at secondary and tertiary facilities, though coding accuracy and completeness vary by facility type and staffing levels. Laboratory data, particularly from the National Public Health Laboratory network and the Kenya Medical Research Institute (KEMRI) laboratory system, is progressively being digitised and linked to clinical records.
For external research organisations and data partners such as Kapsule, the practical implication is that Kenya produces a volume and diversity of structured health data that is unusual for a low-middle-income country. The combination of OpenMRS-origin records, DHIS2 aggregate data, and mobile health platform outputs creates a layered data environment that can support feasibility studies, epidemiological research, and health economics analyses, provided the data is properly aggregated, de-identified, and quality-scored before use.
Clinical Research Capacity and Trial Activity
Kenya is one of sub-Saharan Africa's most active clinical trial markets. The Kenya Medical Research Institute (KEMRI) is the country's premier research body, operating over a dozen research centres and stations across the country. KEMRI-Wellcome Trust Research Programme, based in Kilifi on the Kenyan coast, is one of the most productive health research collaborations in Africa, generating peer-reviewed output across infectious diseases, genomics, health systems, and paediatric medicine. The KEMRI-CDC collaboration in Kisumu has been central to HIV, malaria, and TB research for decades.
Academic medical centres contribute substantially to research output. The University of Nairobi's College of Health Sciences, Moi University School of Medicine (which hosts the AMPATH consortium), and Aga Khan University's East Africa campus all maintain active research programmes with international collaborations.
ClinicalTrials.gov listings show Kenya consistently ranking among the top five African countries by number of registered trials, covering a broad therapeutic range including HIV, oncology, maternal health, respiratory disease, and vaccines. The country's participation in global vaccine trials, including trials for COVID-19, malaria (RTS,S), and other candidates, has further strengthened its regulatory and clinical trial infrastructure.
The Pharmacy and Poisons Board (PPB), recently reconstituted as the Kenya Pharmacy and Poisons Authority, regulates clinical trials and drug approvals. While regulatory timelines can be variable, the PPB is generally considered one of the more experienced and capable regulatory bodies in East Africa. The National Commission for Science, Technology, and Innovation (NACOSTI) issues research permits for foreign investigators, and ethics review is conducted through accredited Institutional Ethics Review Committees (IERCs) at research institutions and hospitals.
For a comparative perspective on research infrastructure across the region, Kenya's trial capacity complements that of Rwanda's highly centralised system and Ethiopia's rapidly expanding research network, while sharing certain regulatory parallels with Nigeria's larger but more fragmented research environment.
Opportunities for Data-Driven Health Innovation
Kenya's combination of digital health maturity, research infrastructure, and policy ambition creates several distinct opportunities for organisations working in health data and analytics.
Universal Health Coverage data needs. As Kenya scales its UHC programme through the Social Health Authority, the demand for actuarial data, disease costing models, and population health analytics will intensify. Organisations that can provide structured, longitudinal health records to support benefits package design and claims adjudication will find a receptive market.
Real-world evidence generation. The density of EMR-origin data in Kenya makes it one of the few African countries where retrospective real-world evidence (RWE) studies are feasible at meaningful scale. Pharmaceutical companies evaluating treatment patterns, drug utilisation, or outcomes for marketed products can draw on Kenyan EHR data as a complement to traditional clinical trial evidence.
Precision public health. County-level health planning in Kenya requires granular data on disease prevalence, health service utilisation, and resource allocation efficiency. The 47-county structure creates natural demand for subnational analytics products that go beyond national averages, a capability that requires facility-level data aggregation and spatial analysis.
Clinical trial site selection and feasibility. Kenya's position as a top-tier trial destination in Africa means that site identification, patient population estimation, and enrollment forecasting are recurring needs. Access to aggregated, de-identified patient records can compress feasibility timelines from months to weeks, a value proposition that Kapsule's platform is specifically designed to deliver for East African markets.
Health financing and insurance analytics. With private health insurance penetration growing and the Social Health Authority expanding public coverage, insurers and payers need claims-linked clinical data for product design, fraud detection, and risk stratification. Kenya's mixed public-private delivery model generates the data diversity needed for these applications.
Kenya still faces real challenges. Data fragmentation across county systems, variable coding quality, health workforce constraints, and incomplete interoperability all limit what can be achieved today. Even so, Kenya's health data infrastructure is maturing rapidly, and the country is positioning itself as the data backbone of East Africa's health economy. Organisations that build partnerships and data access agreements now will be best positioned as the ecosystem continues to develop.
Kapsule provides access to structured, de-identified health records covering over 75 million patients across 9 African countries. Contact our team to discuss how Kenyan health data can support your research, site selection, or market analysis.
This article is intended for informational purposes only and does not constitute legal, medical, or regulatory advice. Readers should obtain independent professional counsel for their specific circumstances.