BACKGROUND: Major congenital malformations place a considerable burden on the affected child, the family and society. Any kind of medicine used during pregnancy might have a harmful impact; therefore, such practice has raised concerns. The objective of the current study was to explore the relationship between the use of herbal medicines by pregnant women during the first trimester of pregnancy and the risk of major congenital malformation in their live born infants. METHODS: This was a cross-sectional analysis of data from a prospective pregnancy cohort, which was established between 1984 and 1987. To assemble the cohort, pregnant women of >or=26 weeks of gestation who came to the Taipei Municipal Maternal and Child Hospital in Taiwan for prenatal care were enrolled in the study and interviewed using a structured questionnaire. Detailed information, including herbal medicine use during different periods of pregnancy, was obtained during the interview. Past medical history, current obstetric data and details on conventional medicines used during pregnancy were abstracted from medical records. Data on birth weight, gestational duration and characteristics of live born infants were gathered from the Taiwan national birth register. Congenital malformation information was obtained from multiple sources: the newborn examination record (1984-7); the national death register (1984-2003); and Taiwan National Health Insurance data (1996-2000). Multiple logistic regression was used to estimate the odds ratio [OR] of major congenital malformation by herbal medicines used during the first trimester. RESULTS: A total of 14,551 live births were analysed. After adjustment for confounding factors, taking huanglian during the first trimester of pregnancy was found to be associated with increased risk of congenital malformations of the nervous system (adjusted OR 8.62, 95% CI 2.54, 29.24). An-Tai-Yin was associated with an increased risk of congenital malformations of the musculoskeletal and connective tissues (adjusted OR 1.61, 95% CI 1.10, 2.36) and the eye (adjusted OR 7.30, 95% CI 1.47, 36.18). CONCLUSION: We found evidence for a possible link between the use of specific herbal medicines during the first trimester of pregnancy and increased risks of specific groups of congenital malformations. We could not investigate whether the adverse effects were related to direct toxicity from the herbal medicines, or were from misuse, contamination or uncontrolled confounding. Nonetheless, we would advise caution regarding use of herbal medicines during pregnancy, and we suggest that further investigation of these findings is warranted.