BACKGROUND: The prevalence of hepatitis B (HBV) carriage in Mongolia is reported to be 14%. Universal HBV immunization of newborns has been shown to decrease carriage in Asian populations. Mongolia began universal newborn vaccination in 1991. This evaluation of vaccine coverage and effectiveness compares the success of the program between urban and nomadic rural populations. METHODS: Using random cluster sampling, 148 Mongolian 2-year-olds from seminomadic rural families were compared with 127 2-year-olds from Ulaanbaatar, the capital city. RESULTS: More than 95% of all subjects received hepatitis B vaccine although rural subjects were less likely to complete the series than were urban subjects. Adequate vaccine response differed significantly: 94.2% of urban subjects versus only 70.2% of rural subjects had protective anti-HBs levels (P < 0.001). Overall the proportion of hepatitis B infection in both samples was lower than the historical Mongolian prevalence. However, unexpectedly 40% of subjects in