Objective: To determine the prevalence of the hepatitis B viral (HBV) infection and hepatitis B e antigen (HBeAg) positivity among pregnant women attending antenatal clinics in two referral hospitals in northern Uganda.

Design: Cross-sectional observational study.

Setting: Two tertiary hospitals in a postconflict region in a low-income country.

Participants: Randomly selected 402 pregnant women attending routine antenatal care in two referral hospitals. Five women withdrew consent for personal reasons. Data were analysed for 397 participants.

Primary outcome: Hepatitis B surface antigen (HBsAg) positivity.

Results: Of 397 pregnant women aged 13–43 years, 96.2% were married or cohabiting. 47 (11.8%) tested positive for HBsAg; of these, 7 (14.9%) were HBeAg positive. The highest HBsAg positivity rate was seen in women aged 20 years or less (20%) compared with those aged above 20 years (8.7%), aOR=2.54 (95% CI 1.31 to 4.90). However, there was no statistically significant difference between women with positive HBsAg and those with negative tests results with respect to median values of liver enzymes, haemoglobin level, absolute neutrophil counts and white cell counts. HIV positivity, scarification and number of sexual partners were not predictive of HBV positivity.

Conclusions: One in eight pregnant women attending antenatal care in the two study hospitals has evidence of hepatitis B infection. A significant number of these mothers are HBeAg positive and may be at increased risk of transmitting hepatitis B infection to their unborn babies. We suggest that all pregnant women attending antenatal care be tested for HBV infection; exposed babies need to receive HBV vaccines at birth.