Across Kenya, laboratories play a vital role in the health system—supporting over 70% of clinical decisions and forming the foundation for disease surveillance and epidemic response. With a growing network of more than 10,000 facilities across public, private, and faith-based sectors, Kenya has made major strides in expanding diagnostic services—especially in high-volume testing for HIV and TB. This progress has enabled advanced testing, including early infant diagnosis and drug resistance monitoring, across all 47 counties.
Despite these gains, Kenya’s laboratory system has not yet fully transitioned from vertical, disease-focused investments to a more integrated and resilient national network. While targeted programs have built strong capacity in 15 molecular labs, many challenges persist, including uneven infrastructure, underfunding, and heavy reliance on donors. As the country advances toward Universal Health Coverage (UHC), there is an urgent need to address systemic gaps in coordination, data use, and financial sustainability.
Persistent Challenges Across the Laboratory Ecosystem in Kenya include:
These challenges collectively weaken the health system’s ability to detect, respond to, and manage infectious and emerging diseases. Delayed diagnoses and treatment disruptions leave communities vulnerable, affecting efforts to control HIV, TB, malaria, and emerging health threats such as antimicrobial resistance and outbreaks like COVID-19.
To build a quality-driven, resilient, and nationally integrated laboratory ecosystem that safeguards the health of all Kenyans, the Sustainable Laboratory Quality Systems (SLQS) Project was established to bridge existing gaps. The initiative strengthens Kenya’s diagnostic landscape for HIV, TB, and emerging health threats through robust quality management, expanded molecular testing capacity, digital innovation, and strengthened local ownership.
Amref works with the National Public Health Institute (NPHI) and the National Public Health Laboratories (NPHL) to strengthen the management and coordination of Kenya’s laboratories. This includes transitioning previously donor-supported activities and systems to national leadership to strengthen collaboration between government agencies further, ensure accountability, and maintain the continuity of quality diagnostic services.
To bring testing closer to people, the project expands access to diagnostics for HIV, TB, HPV, and other diseases through decentralised laboratory placement and multi-disease integration. New advanced testing machines, such as Alinity from Roche and Hologic, are now operational in Migori, Busia, and Kisumu, including Kenyatta University Teaching, Referral and Research Hospital, enabling faster and more timely access, more accurate disease detection, quality molecular diagnostic services, and also strengthening surveillance efforts for any emerging health threats. Multi-disease testing has also been introduced, allowing a single platform to test for multiple diseases simultaneously.
Through diagnostic network optimisation (DNO), samples and results now move quickly and safely between counties, health facilities, and reference laboratories, using remote logging, mapped, and coordinated routes, ensuring efficiency, reduced equipment downtime, and the redistribution of workload to clear backlogs. This, coupled with the lab-clinical interface, ensures that results are jointly reviewed by laboratory staff and clinicians, peer-to-peer mentorships are conducted, and inter-lab twinning for skills transfer is undertaken. This has reduced sample rejection rates to less than 0.5% with Busia and Homa Bay achieving more than 75% digital tracking of specimens.
The project encourages ongoing enhancements in laboratory testing processes, ensuring greater accuracy and dependability. Over 600 health facilities have achieved advanced levels of quality improvement, and 158 laboratories have gained full accreditation. Strengthening of KNEQAS for Quality assessments (EQA) panel production for HIV/TB through offering technical and infrastructural support, accreditation as a proficiency testing provider and expanding it to incorporate production of new TB diagnostic tools such as Truenat and LF-LAM in addition to other disease scopes. The project implements laboratory continuous quality improvement (LCQI) and Rapid Test continuous quality improvement (RTCQI) for quality laboratory management systems in over 1,900 health facilities.
To ensure sustainability, PEPFAR-funded staff are being transitioned to government payrolls, while over 1,500 laboratory professionals have been trained in quality management, biosafety, and advanced diagnostics. In partnership with MOH, various training sessions have been converted into e-courses hosted on the MOH Virtual Academy, ensuring ongoing training across the country. The project has also partnered with KMTC to transition practicum sections of the safe-phlebotomy training to be offered on the campuses.
To keep people, animals, and the environment safe, the project prioritises biosafety, biosecurity, and waste management initiatives to ensure proper storage, designation, treatment, and disposal of chemical and other laboratory waste. The project provides safe working conditions in laboratories by certifying over 300 biosafety cabinets and other auxiliary equipment, ensuring they are regularly maintained and calibrated in accordance with national standards, and supporting the national calibration centre in maintaining ISO 17025. Sustainable Financing for Laboratories
Laboratory services are now being included in county health budgets and supported through national financing frameworks such as the Facility Improvement Fund (FIF) and the Social Health Authority (SHA). Twenty-five counties are developing financing roadmaps to keep laboratory services running even after donor funding ends.
The project is modernising Kenya’s laboratories by developing and implementing integrated digital systems, such as ePT, and by creating an in-country FHIR integration guide for aligning health information management systems with PHC and the national digital superhighway. This digital integration enables real-time data exchange, thereby improving disease monitoring, enabling quicker decision-making, and enabling the use of predictive analytics to spot potential outbreaks early.
The Sustainable Laboratory Quality Systems (SLQS) Project is revolutionising how Kenya detects and responds to diseases. By enhancing the management, connectivity, and funding of laboratories, the project ensures that Kenyans receive quicker, more precise, and more reliable test results, regardless of their location.
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Efficient transport of laboratory specimens is critical for timely diagnosis and effective treatment. In Kenya — a country with over 13,000 health facilities spread across 47 counties — delays in moving blood, sputum, and other samples have long affected how quickly patients receive care, especially for HIV, TB, malaria, and other infectious diseases.
To address these challenges, Kenya established the Integrated Specimen Referral System (ISRS) — a unified national framework for collecting, transporting, tracking, and delivering specimens and results across the entire health system. The ISRS replaces fragmented, disease-specific courier systems with a coordinated, multisectoral approach that ensures samples from even the most remote dispensaries reach testing laboratories safely and on time.
Led by the Ministry of Health, in partnership with County Governments, Amref Health Africa in Kenya, CDC, and other stakeholders, the ISRS has now been rolled out in 25 counties. The system uses digital tools such as GPS tracking, barcoded labelling, and real-time dashboards to monitor specimen movement.
In Busia and Homa Bay Counties, for instance, over 75% of health facilities log specimens digitally—cutting turnaround times for TB and HIV test results from around 10 days to less than 5.
The ISRS also promotes the One Health approach, linking human, animal, and environmental laboratories to strengthen disease surveillance and outbreak preparedness. Through this integration, Kenya is constructing a resilient, cost-effective, and data-driven diagnostic network that enhances care quality and bolsters national health security.
Across Kenya, laboratories remain essential for disease detection, treatment, and epidemic control. However, for many years, systemic barriers have limited their capacity to function optimally. Despite significant progress in HIV and TB care, where laboratory testing supports over 70% of clinical decisions, inefficiencies in diagnostic capacity, fragmented governance, and limited digital integration continue to weaken service quality and timeliness.
Kenya’s national laboratory network includes over 10,000 testing sites across public, private, and faith-based sectors, but less than 30% are fully connected to national surveillance or digital reporting systems. Weak links between national and county laboratories, combined with heavy donor reliance and poor infrastructure, have hindered progress towards resilient, locally owned diagnostic systems.
Persistent Challenges Across the Laboratory Ecosystem in Kenya include:
These challenges collectively weaken the health system’s ability to detect, respond to, and manage infectious and emerging diseases. Delayed diagnoses and treatment disruptions leave communities vulnerable, affecting efforts to control HIV, TB, malaria, and emerging health threats such as antimicrobial resistance and outbreaks like COVID-19.
To build a quality-driven, resilient, and nationally integrated laboratory ecosystem that safeguards the health of all Kenyans, the Sustainable Laboratory Quality Systems (SLQS) Project was established to bridge existing gaps. The initiative strengthens Kenya’s diagnostic landscape for HIV, TB, and emerging health threats through robust quality management, expanded molecular testing capacity, digital innovation, and strengthened local ownership.
