To evaluate the impact of maternal HIV-infection on routine childhood Immunisation coverage, we compared the Immunisation status of children born to HIV-infected and HIV-uninfected women in rural Uganda. The study population was 214 HIV(+) and 578 HIV(-) women with children aged 6 to 35 months previously enrolled in a community study to evaluate maternal and child health in Rakai District, Uganda. Sampling of subjects for interview was stratified by the use of voluntary counselling and testing (VCT) service so that the final sample was four groups: HIV + /VCT+ (n = 98); HIV + /VCT- (n = 116); HIV - /VCT+ (n= 348); HIV - /VCT- (n = 230). The main outcome measure was the percent of complete routine childhood Immunisations recommended by the WHO as assessed from Immunisation cards or maternal recall during household interviews. We found that Immunisation coverage in the overall sample was 26.1%. For all vaccines, children born to HIV-infected mothers had lower Immunisation coverage than children born to HIV-negative mothers (21.3 vs. 27.7%). There was a statistically significant interaction between maternal HIV-infection and maternal knowledge of HIV-infection (p = 0.034). The children of mothers who were HIV-infected and knew their serostatus (HIV + /VCT + ) had a more than two-fold odds of underImmunisation (OR = 2.21, 95% CI: 1.14, 4.29) compared to children of mothers who were HIV - /VCT-. We conclude that maternal HIV-infection was associated with childhood underImmunisation and this was mediated by a mother's knowledge of her HIV status. HIV VCT programmes should encourage HIV-infected mothers to complete childhood Immunisation. Improving access to Immunisation services could benefit vulnerable populations such as children born to HIV-infected mothers.