Malaria Hospitalisations in Kenya's Kilifi County Drop by Nearly 98% from 1999 Peak

For decades, a malaria diagnosis was one of the most common reasons a child in Kilifi County, on Kenya's coast, ended up in hospital.

That is no longer true. A new analysis of 35 years of hospital records has found that malaria hospitalisations among children there have fallen to a fraction of what they once were, marking one of the most sustained declines in childhood malaria ever documented on the continent.

The study, led by researchers at the KEMRI-Wellcome Trust Research Programme, a joint Kenyan-British medical research institute based in Kilifi, tracked every child admitted to Kilifi County Hospital between January 1990 and December 2024.

It is one of the longest continuous records of malaria illness anywhere in Africa, covering more than 69,000 children over three and a half decades.

A disease that once filled the children's ward

In 1999, malaria hospitalisation reached its highest point: about 26 out of every 1,000 children in the study area were admitted with malaria that year, and malaria accounted for over half of all children's hospital admissions. By the period 2020 to 2024, that number had fallen to fewer than 1 in every 1,000 children a year, and malaria made up less than 5 percent of admissions.

The decline in deaths was just as steep. In the 1990s, malaria killed about 4 children out of every 10,000 in the study population each year. By 2020-2024, that had dropped to roughly 3 in every 100,000, a fall of about 93 percent.

The researchers also tracked how much malaria infection existed in the wider community, not just among children sick enough to be hospitalised. In the 1990s, more than 1 in 3 children carried the malaria parasite.

By 2020-2024, that had dropped to roughly 1 in 50, a 94 percent fall in exposure.

What changed

The researchers point to two main factors behind the shift: the wide rollout of insecticide-treated bed nets, and improved access to an effective malaria drug combination called artemether-lumefantrine, given to patients as first-line treatment since the mid-2000s.

Bed nets work by physically blocking mosquito bites at night, when the malaria-carrying Anopheles mosquito is most active; earlier research from the same area found net use cut malaria infection in the community by more than half.

The timeline in the study lines up with major shifts in policy.

Kenya, like many African countries, scaled up bed net distribution and switched to more effective malaria drugs during the 2000s, following international commitments made after the continent's malaria burden was declared a crisis at the turn of the century.

The Kilifi data offers a rare, ground-level look at what that global effort actually did to a real population over time, rather than a modelled estimate.

Malaria has not disappeared, and its pattern has shifted

Even with the steep decline, malaria has not gone away in Kilifi.

The researchers found that the children still being hospitalised with malaria today are, on average, older than those hospitalised in the 1990s.

Three decades ago, the typical child hospitalised with malaria was around 19 months old. By the 2012-2019 period, that had risen to around 4 years old.

This shift makes sense once the underlying biology is considered: children who grow up with less exposure to malaria build less natural immunity to it early on, so when they are eventually infected, it can happen later in childhood.

The researchers also found that cerebral malaria, a severe form of the disease that affects the brain and can cause seizures or unconsciousness, now makes up a larger share of serious malaria cases than it used to, compared with severe anaemia, another dangerous complication of malaria. Importantly, this is a shift in proportion, not a rise in numbers.

Both cerebral malaria and severe anaemia cases have kept falling in absolute terms; cerebral malaria has simply fallen more slowly than severe anaemia has.

The authors say this matters for planning, not panic: it means that as malaria becomes rarer, health workers and hospitals may need to stay alert for a somewhat different pattern of severe cases, in slightly older children, rather than assuming young infants remain the group at greatest risk.

How this compares with earlier findings

This is not the first time researchers have tracked malaria's decline in Kilifi. A 2008 study in The Lancet documented falling malaria admissions there between 1990 and 2007.

A 2016 study in PLOS Medicine extended that picture to 25 years, and a 2019 study in BMC Medicine covered 27 years, both from the same hospital and research partnership.

The new analysis extends that same surveillance effort to 35 years and is the longest version of this dataset published so far, allowing the researchers to look further past 2019 into the most recent, lowest-transmission years.

What this means, and what it doesn't

This study is based on one hospital and one surrounding population in coastal Kenya.

It does not mean malaria has disappeared from Kenya as a whole, and other parts of the country, including areas around Lake Victoria in the west, continue to report much higher malaria burdens.

The findings describe what has happened specifically within the Kilifi Health and Demographic Surveillance System, a monitored population of roughly 250,000 people whose hospital visits have been tracked in detail since the 1990s.

It is also worth noting that this research has been shared as a preprint on medRxiv, meaning it has been made public before undergoing formal peer review by other scientists.

Its methods and figures have not yet been independently checked and published in a scientific journal, which is a standard next step for research of this kind.

The findings are consistent with the pattern shown in earlier peer-reviewed studies from the same research group, but they should still be read as preliminary until that review is complete.

The Kilifi data offers a rare long view of what happened when bed nets and better treatment were sustained over decades in one community: a disease that once filled a children's ward has become, in that specific place, a comparatively rare reason for a child to be hospitalised.

Source: Kamau A, Musau MM, Mturi N, Mohammed S, Mwambingu G, Walumbe D, Nyaguara A, Williams TN, Bejon P, Snow RW. Decline to near-zero malaria hospitalisation over 35 years on the Kenyan Coast. medRxiv. 2026. doi:10.64898/2026.07.13.26357922