Background Hepatitis B is a considerable disease burden among Asians. Little is known about its disease behaviour in pregnant women. Methods Clinical, laboratory and radiological data of pregnant and peri-partum females with chronic hepatitis B virus (HBV) infection who were seen between years 1999 and 2004 were studied. Their progress was documented up to 6 months post-partum. This was compared with the age-matched and HBe status-matched, non-pregnant, female patients with chronic HBV infection, who were consecutively selected from the department's registry as controls (ratio 1 mother: 4 non-pregnant controls), over the corresponding period. Results A total of 35 mothers and 140 controls were studied. Mean age of patients was 30.7 +/- 3.6 years. Majority of mothers (74.3%) presented during pregnancy itself. 1st:2nd:3rd trimester presentation = 20.0%:48.6%:5.7%. Majority (65.7%) were positive for HBe antigen (HBeAg) at the time of presentation. About 57.1% mothers had a clinical event in the form of alanine transferase (ALT) elevation and/or loss of HBeAg vs 28.8% among controls (P = 0.002). Among HBeAg-positive subjects, more mothers (14.3%) than controls (2.2%) had resultant HBeAg loss (P = 0.02). Among HBeAg negative subjects, more mothers than controls had serum ALT elevations in the post-partum period (P = 0.007). Overall, more mothers had elevated ALT levels than controls, regardless of their HBeAg status. Neither mothers nor control subjects decompensated clinically, neither required liver transplantation nor died during the study period. Conclusions Pregnancy is associated with serum ALT elevation and HBeAg loss in patients with chronic HBV infection in the peri-partum period.