This prospective case-control study was conducted to investigate the relation between endometrial natural killer CD16+ cells and unexplained infertility. 45 women with unexplained infertility and another 45 fertile women as their controls were recruited in the study. Trans-vaginal sonography and endometrial sampling were performed 5-9 days after ovulation (implantation window). Endometrial thickness and sub-endometrial blood flow indices were assessed, endometrial CD16+ were assessed using immunohistochemical staining. A significant higher incidence of CD16+ positive endometrium was found in infertile women than controls, as well as a highly significant difference between the 2 groups regarding endometrial thickness (being thinner in the infertility group) and both sub-endometrial Doppler parameters (RI and PI) (P<0.001). A positive correlation was found between endometrial positive CD16+ and both endometrial thickness and sub-endometrial RI (P=0.035 and P=0.011 respectively). This study suggests a significant association between endometrial CD16+ NK cells and unexplained infertility.