A cohort of 760 newborns was followed prospectively for 2 years to ascertain the time of administration of childhood vaccinations in rural Malawi and to study predictors of non-compliance with national vaccination recommendations. At 1 year of age, 99% of the infants were fully vaccinated against tuberculosis, 91% against polio, 90% against diphtheria, pertussis and tetanus and 64% against measles. At 2 years, the corresponding vaccination coverages were 99%, 93%, 93% and 84%. On average, all vaccinations were given 1-3 months later than recommended. Many of the delayed measles vaccinations were given during a separate vertical campaign, during which 25% of previously unvaccinated 21-23-month-old children were identified and immunized. Non-compliance with vaccination recommendations was associated with living in villages with no access to mobile vaccination teams, birth between April and June and birth at home. In this rural Malawian area, most vaccination services were functioning well. To increase measles vaccination coverage, regular outreach activities should be encouraged.