In 1969, a small team from the United States Army set up a temporary laboratory on the outskirts of Nairobi. Their brief was to study trypanosomiasis, the sleeping sickness transmitted by the tsetse fly, which was killing people across East Africa. 

The U.S. Army Medical Research Unit-Kenya (USAMRU-K) arrived in Nairobi, operating under the Walter Reed Army Institute of Research. It began as a temporary programme to study trypanosomiasis (sleeping sickness), a deadly disease carried by the tsetse fly. 

Nobody at the time imagined that this modest outpost on the grounds of what is today the Kenya Medical Research Institute (KEMRI) campus off Raila Odinga Way (formerly Mbagathi Road) would be the seed of a relationship that would grow, over five and a half decades, into more than $8 billion of American investment in Kenya’s health system. 

In December 2025, Kenya became the first country in Africa to sign a new bilateral Health Cooperation Framework with the United States in a five-year agreement worth up to $1.6 billion (Ksh208 billion), replacing the funding architecture that had been built, institution by institution, field station by field station, since Walter Reed first arrived in the country. 

USAMRU-K was made permanent in 1973 through a cooperative agreement between the Walter Reed Army Institute of Research and the government of Kenya and later formalised under KEMRI when it was established in 1979. 

From tsetse flies to research infrastructure 

What had begun as a provisional programme became permanent, anchored on a campus that would later become the KEMRI Clinical Research Centre. By 1985, when KEMRI took occupancy of purpose-built laboratory facilities, USAMRD-A headquarters had relocated into that space, cementing the military research presence at the heart of Kenya’s national health research body. 

The US Centres for Disease Control and Prevention arrived in the west of the country in 1979, when Dr Harrison Spencer opened a malaria field centre in Kisumu in response to chloroquine-resistant malaria spreading across East Africa. 

The CDC-KEMRI partnership that grew from that initial outpost anchored at a field station in Kondele would become one of the most productive malaria research partnerships in Africa. Through the 1980s, teams from the station mapped drug resistance patterns, tracked human immune responses, and studied the mosquito vectors that carried the disease across the Lake Victoria basin. 

Between 1992 and 1999, CDC and KEMRI ran the Asembo Bay cohort study, tracking childhood illness across fifteen villages near Lake Victoria in Siaya County, one of the largest longitudinal studies in East Africa at the time and the data backbone for decades of subsequent malaria work. 

In 1999, the US Military HIV Research Program launched an international HIV vaccine programme with KEMRI in the tea highlands of Kericho, founding what became the Kericho Clinical Research Centre. The same year, President Daniel arap Moi declared HIV/AIDS a national disaster. The US launched its Leadership and Investment in Fighting Epidemics (LIFE) Initiative in 2000, the precursor to something far larger. 

PEPFAR and the Architecture of a Generation 

In 2003, President George W Bush announced the President’s Emergency Plan for AIDS Relief during his State of the Union address. Kenya was among the fourteen initial focus countries. 

PEPFAR channelled the bulk of what became more than $8 billion (Ksh1.04 trillion) in US health funding into Kenya over the next two decades. It supported antiretroviral treatment for more than 1.3 million people. It financed approximately 43,000 health workers across the country, including clinical and community staff. It established clinical research centres in Kombewa near Kisumu and in Kericho, the latter becoming, in 2012, the first laboratory in Kenya accredited by the College of American Pathologists, built on a KEMRI/Walter Reed joint model. 

By 2009, the Kisumu Field Station had run a Phase III trial of RTS,S, the first malaria vaccine designed for children, enrolling more than 900 volunteers. 

In 2004, following SARS, the CDC established a Global Disease Detection Centre in Kenya, one of only eleven worldwide and launched the Field Epidemiology and Laboratory Training Programme (FELTP) to build Kenyan capacity in outbreak response. Graduates of that programme would go on to handle over 80 per cent of outbreak investigations detected in the country. 

In 2005, a National Influenza Surveillance and Epidemiology Programme was launched, creating a sentinel system that still feeds respiratory disease data into the global health network. In 2008, Kenya formally joined the President’s Malaria Initiative, expanding CDC and USAID funding for insecticide-treated bed net distribution across the highest-burden counties. 

A research network spanning the country 

By 2013, the US research footprint had spread across the country: Kilifi for dengue research, Kisii for cerebral malaria, Baringo for leishmaniasis, Eldoret for antiviral trials, and Kisian on the shores of Lake Victoria, a continent-class research network co-run with KEMRI. That same year, the CDC helped design and equip the Kenya National Public Health Emergency Operations Centre in Nairobi, the coordinating nerve centre that handles the country’s response when outbreaks strike. 

The partnership deepened in the years that followed. 

In the 2020s, USAMRU-K was formally redesignated as the US Army Medical Research Directorate-Africa, USAMRD-A, a renaming that acknowledged what had become apparent long before: that the Nairobi hub on the KEMRI campus was no longer just a Kenya operation but the anchor for US military medical research across the African continent. 

In 2024, as the two countries marked 45 years of health cooperation, Washington committed $31.1 million specifically to digital health, electronic records systems, solar-powered hospitals, and mobile links to ambulances, layered on top of an annual programme spending of roughly $500 million. The infrastructure of the partnership had grown from a tsetse fly laboratory to a digital health architecture spanning the breadth of the country. 

The Ministry of Health has positioned the deal as a turning point in Kenya’s journey towards health sovereignty. Health Cabinet Secretary Aden Duale framed it as a transition from donor dependency to co-investment, noting that previous arrangements, including PEPFAR and the Global Fund, had created what he described as parallel systems that were costly and fragmented, with as little as 40 per cent of funding reaching frontline workers and commodities. By going government-to-government, the Ministry argued, waste created by implementing partners would be reduced and national ownership strengthened. 

The terms of the handover 

By December 2026, the Kenya Medical Supplies Authority (KEMSA) must be ready to take over the complete procurement and distribution of all health commodities currently managed by US partners. 

By 2028, the government must absorb 13,808 health and laboratory workers, including 13,293 health workers and 515 laboratory staff, onto its public payroll, assuming full financial responsibility for their salaries and benefits. Kenya’s co-financing contributions to the health sector are set to rise sharply: Ksh10 billion in the 2026/2027 financial year, Ksh20 billion in 2027/2028, Ksh35 billion in 2028/2029, and Ksh50 billion in 2029/2030. 

President William Ruto, at the signing ceremony, described the framework as reinforcing his administration’s universal health coverage agenda. 

“Every shilling and every dollar will be spent efficiently, effectively and accountably,” he said, linking the agreement to the rollout of SHA enrolment, the deployment of Community Health Promoters, and the strengthening of KEMSA’s last-mile delivery. 

CS Duale confirmed that shared health data would be governed by the Data Protection Act 2019 and the Digital Health Act 2023, that only de-identified and aggregated data would be transferred, and that formal requests for data access would require approval from the Digital Health Authority and the Data Commissioner. Kenya, he said, retains sole ownership of all health data and associated intellectual property. 

The question that will define the next chapter 

The agreement now asks that this infrastructure, built on American capital, embedded in American-designed systems, and staffed in significant part by workers whose salaries have been paid from Washington, be transferred to Kenyan ownership within five years. 

The story that began in 1969 with a temporary laboratory for sleeping sickness has arrived at a moment where the terms of the relationship are being renegotiated in courts, in parliaments, and in the records of a healthcare system that, over half a century, was built, more than any other single source can claim, on American dollars. 

Whether that system now has the foundations to stand on its own terms, within five years, is the question that will define the next chapter. 

Sources: US Embassy in Kenya, CDC Kenya, KEMRI, Ministry of Health Kenya; Think Global Health, Carnegie Endowment for International Peace, KELIN Kenya, UNAIDS, KFF, WHO Africa, AVAC Global Health Watch, ProPublica and HHR Journal. 

Data analytics & visualisation: Stanley Njihia 
Text: Yvonne Kawira