The purpose of this study was to determine if a comprehensive flow cytometry panel could be used to assess immunophenotype profiles in menstrual blood of patients experiencing reproductive failure and age-matched controls of proven fertility. Menstrual blood samples of 58 recurrent pregnancy loss and repeated implantation failure patients, along with 15 age-matched controls of proven fertility, were obtained within the first 24 h of the onset of menstruation to non-invasively assess the local immunophenotype. Using a comprehensive multi-parameter flow panel, the lymphocyte sub-populations were described and compared. In relation to well-established peripheral blood immunophenotyping values, distinct lymphocyte population differences were noted between the subgroups. The ratios of CD4+ and CD8+ T-cells were inverted in relation to peripheral blood, and uterine natural killler (NK) cells represented by CD56bright were distinctly visualised, emphasising the distinction between menstrual and peripheral blood. In relation to controls, there were marked increases in CD3+ve T-cells (P = 0.009), CD4:CD8 ratio (P = 0.004), CD19 B-cells (P = 0.026) and CD56dim NK cells (P = 0.002) in the reproductive failure cases. The study shows that flow cytometric evaluation could provide a rapid and objective analysis of lymphocyte subpopulations in many forms of tissue and fluid. The findings show significant variations in cellular composition of immune cells indicating a distinct compartment, with differences between cases and controls. Immunological assessment of the menstrual blood immunophenotype, in clinically appropriate patients, may provide insight into the aetiology of adverse reproductive outcome, without the risks and inconveniences associated with a more invasive endometrial biopsy. Lay summary Unexplained infertility is a difficult issue for patients and physicians, but despite diagnostic strides and innovative methods, there are no clear solutions. The involvement of an overactive or underactive immune system in selected cases is undeniable, and the endometrial lining is the most relevant area for investigation because this is where the embryo implants. Endometrial investigations, however, are highly invasive, involve medication and have to be done at the right time. The method described and evaluated here is an alternative assessment which avoids these difficulties and can be used in a clinical setting.