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Objectives To assess whether bacterial vaginosis affects the rates of conception and miscarriage in the first trimester.Design Cohort study.Setting Assisted conception unit of a teaching hospital in Leeds.Participants 867 consecutive women undergoing in vitro fertilisation.Interventions Screening for bacterial vaginosis with a Gram stained vaginal smear before egg collection.Main outcome measures The presence of bacterial vaginosis or normal vaginal flora, and the rate of conception and miscarriage in the first trimester.Results 190 of 771 (24.6%) women had bacterial vaginosis. No difference in conception rate was found between those women with bacterial vaginosis and those with normal vaginal flora: 61 women (32.1%) and 146 of 493 women (29.6%) respectively (relative risk 1.08, 95% confidence interval 0.85 to 1.39; odds ratio 1.12, 0.77 to 1.64). However, 22 women (31.6%) with bacterial vaginosis who conceived had a significantly increased risk of miscarriage in the first trimester compared with 27 women (18.5%) with normal vaginal flora (crude relative risk 1.95, 1.11 to 3.42; crude odds ratio 2.49, 1.21 to 5.12). This increased risk remained significant after adjustment for factors known to increase the rate of miscarriage: increasing maternal age, smoking, history of three or more miscarriages, no previous live birth, and polycystic ovaries (adjusted relative risk 2.03, 1.09 to 3.78; adjusted odds ratio 2.67, 1.26 to 5.63).Conclusions Bacterial vaginosis does not affect conception but is associated with an increased risk of miscarriage in the first trimester in women undergoing in vitro fertilisation, independent of other risk factors.