Background/Objectives: Menstrual blood, a periodic uterine discharge, represents a non-invasive source for an indication of the functional status of the endometrium. While menstrual blood-derived stem cells have been extensively characterized and menstrual blood is considered a diagnostic material for the analysis of gynecologic pathology in research studies, it is not routinely used in clinical settings. To develop novel noninvasive diagnostic tools for endometrial status assessment, we aimed to characterize the morphological and molecular markers of menstrual blood. Methods: Menstrual blood samples were obtained from healthy volunteers and characterized macroscopically and microscopically using smears (May-Grunwald-Giemsa staining), confocal microscopy, and imaging flow cytometry (cluster of differentiation [CD]90, CD45, fibrin). Clot dissociation was performed to analyze the cellular composition of clots. Results: We morphologically characterized menstrual blood cells and identified three uterine-derived cells and cell cluster types (endometrial stromal, endometrial epithelial, and vaginal epithelial). Additionally, we confirmed the specificity of CD90 for endometrial stromal cell populations, which were separately characterized in the supernatant and menstrual blood clots using light and confocal microscopy, and we analyzed the composition of the menstrual blood supernatant and dissociated clots using imaging flow cytometry. Conclusions: The results of this study may serve as a foundation for the development of new non-invasive diagnostic tools for endometrial pathology for the potential support or replacement of highly invasive procedures, such as diagnostic dilation and curettage.