Objectives To determine if the presence of microorganisms in follicular fluid of women undergoing in vitro fertilization-embryo transfer (IVF-ET) adversely affects the outcome of the treatment cycles. Methods Follicular fluid was collected from 86 women enrolled for IVF-ET at the National Hospital, Abuja from June 1, 2018 to December 1, 2018. Microscopy imaging and cultures were performed to identify bacteria and fungi in the follicular fluid and the vagina. Women with follicular fluid microorganisms were the test group while the controls were those without follicular fluid microorganisms. Fertilization and pregnancy rates were subsequently determined and their association with the presence of follicular fluid microorganisms was assessed using univariable and multivariable logistic regression modelling. Results The mean age and mean Body Mass Index (BMI) of the participants were 35(± 3.5) years and 28(± 4.9) kg/m.sup.2 respectively. Bacteria and fungi were isolated in 17% of the follicular fluid samples collected (n = 15/86). Most common isolates were Streptococcus spp. (n = 4/15), Staphylococcus aureus (n = 7/15), Enterococcus spp. (n = 4/15), Lactobacillus species (n = 2/15) and Candida albicans (n = 2/15). There was no statistically significant difference in the fertilization rates (adjusted odds ratio [AdjOR] 0.55, 95% confidence interval [CI] 0.04-7.34; P = 0.10) and pregnancy rates (AdjOR 4.02, 95% CI 0.56-28.92; P = 0.19) between the group of women with positive follicular fluid bacterial /fungal colonization as compared against those with negative follicular fluid colonization. Conclusion Isolation of microorganisms from follicular fluid did not adversely affect fertilization and pregnancy rates following IVF-ET treatment cycles at the fertility centre of National Hospital, Abuja.