Years of vaccine shortages have left Kenya struggling to keep routine childhood immunisation on track, with a new WHO and Unicef report showing thousands of children missed life-saving vaccines and are now at greater risk of preventable diseases.
The latest estimates released by the World Health Organization (WHO) and Unicef show childhood vaccination coverage in Kenya has declined since reaching its highest levels in 2021, with repeated shortages disrupting immunisation services over the past five years.
The biggest drop was recorded in the rotavirus vaccine, which protects infants against severe diarrhoea and vomiting. Coverage for the final dose fell from 95 per cent in 2021 to just 29 per cent in 2022.
The report attributes the sharp decline to prolonged vaccine shortages, stating, “Programme reports 9.8 months vaccine stockout at national and subnational levels.”
Rotavirus is among the leading causes of severe diarrhoea in young children and can cause dangerous dehydration. Without prompt treatment, the illness can become fatal.
The vaccine shortage has continued to affect immunisation services.
In March, the Ministry of Health warned that Kenya was close to running out of Rotavac, the vaccine used to protect babies against rotavirus.
Health CS Aden Duale said delays at the factory manufacturing the vaccine had affected supplies.
“The Ministry of Health is closely monitoring stock levels and coordinating with partners to restore normal supply as soon as possible,” he said.
At the time, the country had only about 4,000 doses remaining, enough to last for less than one month.
The shortages were also evident in June 2025 when the Ministry of Health announced that 12 of the country's 47 counties had completely run out of vaccines.
Stocks of the BCG vaccine, which protects children against tuberculosis, and the polio vaccine had dropped to only two weeks' supply.
Medical Services PS Ouma Oluga said the government had introduced measures to ensure children continue receiving routine vaccinations.
“We have put in place the Zero-Dose Catch-Up Mechanism under the Bottom-Up Economic Transformation Agenda (BETA) to ensure no child misses a single dose of any vaccine,” he said.
The WHO's Immunisation Agenda 2030 sets a target of at least 90 per cent national coverage for all basic childhood vaccines.
However, the latest WHO and Unicef report shows Kenya is yet to meet that target in several areas. Coverage for the measles vaccine dropped from 92 per cent in 2019 to 80 per cent in 2025, while vaccines protecting children against diphtheria, tetanus and whooping cough also recorded lower coverage.
The government says it is taking steps to prevent future shortages after the National Treasury more than doubled the vaccine budget to Sh4.6 billion for the financial year that began in July.
Gavi, which supports vaccine access in low-income countries, reported that many countries recorded better childhood vaccination coverage in 2025.
Kenya's latest figures, however, present a mixed picture. Coverage for the BCG vaccine improved slightly to 88 per cent from 87 per cent the previous year, while second-dose measles vaccination rose from 76 per cent in 2024 to 81 per cent.
Despite those gains, coverage for vaccines against polio, hepatitis B, whooping cough and rotavirus registered slight declines.
WHO and Unicef cautioned that the latest estimates should not be directly compared with previous reports because vaccination figures are reviewed every year as new information becomes available.
The organisations added that findings from an ongoing national health survey could result in further adjustments when the next report is released in July 2027