Women who fail to conceive have differences in lymphocyte population in peripheral blood, peritoneal fluid and follicular fluid (FF) compared with fertile women. Leukocyte subsets in FF from patients with endometriosis may affect folliculogenesis and oocyte maturity. The aim of our study was to investigate T lymphocytes (T), Natural killer cells (NK) and Natural killer T cells (NKT) population and their activity in the follicular fluid of infertile women, and to evaluate the impact of those immune cells on embryo quality. The lymphocyte population present in follicular fluid was quantified by cytometric analysis, using fluorochrome-conjugated monoclonal antibodies. The preparation of the samples for flow cytometry was performed according to the recommendations of the manufacturer (BD Biosciences, Sent Jose, USA). Prepared samples were analysed using FACSCalibur flow cytometer (Becton Dickinson, USA). Altogether 37 follicular fluid samples were investigated. Infertility reasons in the study population were as follows: 15 tubal infertility and 8 endometriosis cases. In the follicular fluids of women with tubal infertility there were a lesser count of CD56⁺69⁺ cells compared with the control group. An increase in CD56⁺16⁺ cell count indicated better embryo quality. Immune cells participating in the pathogenesis of genital system disorders may influence fertility of women. Severe inflammation might lead to a decrease in NK cell activity. The amount of NK cells (CD56⁺16⁺) in follicular fluid correlates with the morphological characteristics of embryo (r = 0.276; p = 0.006).