Purpose This study was designed to examine the effect of bacterial contamination on in vitro fertilization treatment outcomes. Method In a prospective clinical trial, 152 patients aged 23-38 years, mean 33.3±4.6, undergoing IVF treatment were selected for this study. During embryo transfer, separate samples were collected for microbial examination from the following sites: the fundus of the vagina, the cervix, the embryo culture medium prior and post-embryo transfer, the tip of the catheter, and the external sheet. All the samples were separately cultured to identify any bacteria or yeast present. Results Pregnancy rates in patients testing positive for Entrobacteriaceae (22.2% versus 51%) and Staphylococcus species (17.6% versus 44%) were significantly lower than those in the negative culture group ( p< 0.001). The pregnancy rates do not seem to be affected by the other isolated microorganisms.Conclusion This study shows that the presence of vaginalcervical microbial contamination at the time of embryo transfer is associated with significantly decreased pregnancy rates.