Comprehensive understanding of endometriosis immune pathophysiology in different hormonal milieu and disease severity has been hampered by limited direct characterization of immune populations in endometrium, blood, and lesions. Simultaneous deep phenotyping at single-cell resolution of complex tissues has transformed our understanding of the immune system and its role in many diseases. Herein, we report mass cytometry and high dimensional analyses to study immune cell phenotypes, abundance, activation states, and functions in endometrium and blood of women with and without endometriosis in different cycle phases and disease stages. This dataset contains two types of datasets. One for the broad panel (n=17, all endometrial samples) and one for the focused panel (n=39, n=31 for endometrium and n=26 for PBMC). We have included here a metadata excel file for each panel. In addition, we have also included the two CyTOF panels used in this study, which indicate the channels and markers for each channel. For the brad panel, the fcs. files contain CD45+ manually gated live cells. For the focused panel, cells were manually gated obtaining myeloid cells (and a cluster of putative B cells). The files contain cells that are live CD45+, CD3-, CD66b-, CD56-, and CD56-. Included are focused panel dataset.