Objective The study was conducted to determine the prevalence pattern of birth defects in Zhoushan Archipelagoes,Zhejiang province, providing evidence for the development of preventive strategies to reduce the incidence of birth defects in the region. Methods Population based retrospective analysis was conducted based on the surveillance data tracking birth defects in Zhoushan archipelagoes from 2000 to 2006. Results Given a total of 498 birth defects out of 41 396 fetuses in the surveillance, the average prevalence in Zhoushan was 120.30/10 000 from 2000 to 2006, and a rising trend was shown of individual defects by year. Common types of birth defects in Zhoushan included congenital heart diseases (33.58/10 000),external ear malformation (16.19/10 000), polydactyly (15.46/10 000), cleft lip with or without cleft palate (11.60/10 000),congenital hydrocephaly (10.39/10 000). Ventricular septal defect, atriotricular septal defect and patent ductus arterious were most commonly presented congenital heart conditions. Conclusion Congenital heart diseases are highly prevalent birth defects in Zhoushan, and intervention considerations should be given.