One of the consequences of the HIV/AIDS epidemic in sub-Saharan Africa is the increase in the number of orphans, estimated to have reached 6–11% of children <15 years old in 2000. Orphans who stay in their communities may be at increased risk for poor health due to reduced circumstances and loss of parental care. We have used data from a population-based study in rural western Kenya to compare basic health and nutritional indicators between non-orphaned children <6 years old and children who lost either or both of their parents. In June 2000, all children <6 years old who had been recruited for a cross-sectional survey in 60 villages of Rarieda Division, western Kenya, in June 1999 were invited to return for a follow-up survey. Basic demographic characteristics, including the vital status of the child's parents, and health histories were requested from all 1190 participants of the follow-up survey, along with a finger-prick blood sample for determination of malaria parasite status and haemoglobin (Hb) levels. Height-for-age (H/A) and weight-for-height (W/H) Z-scores were also calculated from anthropometric measurements. Overall, 7.9% of the children had lost one or both their parents (6.4% had lost their father, 0.8% had lost their mother and 0.7% had lost both parents). While there was no difference between orphans and non-orphans regarding most of the key health indicators (prevalence of fever and malaria parasitaemia, history of illness, Hb levels, H/A Z scores), W/H Z-scores in orphans were almost 0.3 standard deviations lower than those of non-orphans. This association was more pronounced among paternal orphans and those who had lost a parent more than 1 year ago. These results suggest that the health status of surviving orphans living in their community is similar to that of the non-orphan population, but longitudinal cohort studies should be conducted to determine better the overall impact of orphanhood on child health.