VaccinationThousands of children in Kenya have been left vulnerable to deadly childhood diseases after repeated vaccine shortages disrupted immunisation programmes over the past five years.
The shortages affected vaccines that protect babies from illnesses that can quickly become life-threatening, including rotavirus, which causes severe diarrhoea and vomiting, measles and whooping cough.
New global data from the World Health Organization (WHO) and Unicef shows Kenya’s childhood vaccination coverage has declined since 2021, after reaching its highest levels during that period.
The rotavirus vaccine recorded the sharpest drop. Coverage for the final dose fell from 95 per cent in 2021 to just 29 per cent in 2022.
The report attributes the dramatic decline to prolonged vaccine shortages, noting, “Programme reports 9.8 months vaccine stockout at national and subnational levels.”
For infants, the consequences can be severe. Rotavirus can cause dangerous dehydration through diarrhoea and vomiting, and without timely treatment, it can lead to death.
The shortage has continued to affect vaccination services.
In March, the Ministry of Health warned that Kenya was nearly out of Rotavac, the vaccine used to protect babies against rotavirus.
Health CS Aden Duale said the shortage was caused by delays at the factory that manufactures the vaccine.
“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, Kenya had only about 4,000 doses remaining countrywide, enough for less than one month.
The situation was also critical in June 2025, when the Ministry of Health reported that 12 of Kenya’s 47 counties had completely run out of vaccines.
Stocks of the BCG vaccine, which protects children against tuberculosis and the polio vaccine had fallen to only two weeks of supply.
Medical Services PS Ouma Oluga said the government had introduced measures to ensure children do not miss 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 targets at least 90 per cent coverage for all basic childhood vaccines nationally.
However, the latest WHO and Unicef report shows Kenya is falling short in several areas.
Measles vaccine coverage dropped from 92 per cent in 2019 to 80 per cent in 2025, while coverage for vaccines protecting against diphtheria, tetanus and whooping cough has also declined.
The government says it is working to prevent future shortages. The National Treasury has more than doubled the vaccine budget to Sh4.6 billion for the financial year starting in July.
Gavi, which supports vaccine access in low-income countries, said many countries recorded improvements in vaccination coverage in 2025.
Kenya’s latest figures show a mixed picture. BCG vaccine coverage improved slightly to 88 per cent from 87 per cent the previous year, while second-dose measles vaccination increased to 81 per cent from 76 per cent in 2024.
However, coverage for several other vaccines, including polio, whooping cough, hepatitis B and rotavirus, recorded slight declines.
WHO and Unicef cautioned the figures should not be directly compared with previous reports because vaccination estimates are revised annually as new data becomes available.
The organisations said results from an ongoing national health survey in Kenya could further adjust the figures when the next report is released in July 2027.
Instant analysis
Kenya’s declining childhood vaccination coverage presents a serious public health concern because diseases that vaccines prevent can spread quickly and become fatal, especially among infants. The repeated shortages point to weaknesses in vaccine supply chains, planning and distribution systems. While increased government funding and catch-up programmes may help restore coverage, sustained availability of vaccines remains critical to protecting children. The mixed performance across different vaccines shows progress is possible but fragile. Strengthening procurement systems, improving county-level stock monitoring and ensuring parents have confidence in immunisation programmes will be essential to prevent avoidable illnesses and protect future generations.
