The present study prospectively assessed pregnancy outcome of women taking probiotics during the periconceptional period. A group of 104 women who had taken Lactobacillus in early pregnancy and 200 age- and parity-matched control pregnant women exposed to non-teratogenic agents were also recruited into the study and followed-up prospectively. Median gestational age of women exposed to Lactobacillus was 5.2 (range: 1.9-17.6) weeks. Exposure was at a mean dose of 510 mg/day for a median of 4.0 days (range: 1-90 days). In the exposed group, pregnancy outcomes included 96 live births and eight spontaneous abortions versus 187 live births and 21 spontaneous abortions in the non-exposed group. There was no statistical difference in adverse pregnancy outcomes, including the number of spontaneous abortions, pre-term births as well as a low birth weight between the two groups (p > 0.05). In the exposed group, there were two (2.1%) major congenital malformations in comparison with five (2.7%) in the comparison group (p = 0.7). In conclusion, no association was identified between ingestion of Lactobacillus in early pregnancy for a limited period of time and adverse pregnancy outcomes. However, rare pregnancy outcomes may have been missed due to the limited sample size included in the study.