The activation, growth and maturation of oocytes to an ovulatory phase, termed folliculogenesis, is governed by the orchestrated activity of multiple specialized cells types within the ovary, yet mechanisms governing diversification and behavior of discrete cellular sub-populations within follicles are poorly understood. We set out to identify and characterize unique subsets among the granulosa (GC), theca (TC) and stromal cell fractions, and to compare the molecular profiles of these sub-populations when isolated from native ovarian versus xenograft-derived antral follicles. Small antral follicles (< 5mm) were isolated from ovaries of organ donors or patients undergoing whole ovarian resection for fertility preservation. These were compared to antral follicles that developed in long term (> 14 weeks) xenografts of cryopreserved/thawed human ovarian cortex. Immunostaining, flow cytometry, bulk and single-cell RNA sequencing were used to segregate and interrogate discrete follicle-derived cell fractions. The GC fraction was first purified from 3 small (2-3 mm) ovary-derived antral follicles and subjected to bulk RNA sequencing to identify candidate surface molecules that may specifically identify follicle cell sub-types. Candidate factors were screened using immune-staining and flow cytometry of xenograft and ovary-derived follicles. 22 unique single-cell library preparations (∼100,000 cells) representing fractions from 13 individual follicles (8 ovary origin, 5 xenograft origin) and 6 women were prepared, sequenced and analyzed. Analysis of GC, TC and stromal subpopulations deconstructed phenotypic diversification during early antral follicle development, identifying secreted factors that are differentially enriched between mural and oophorus GCs, and segregating stromal/support and steroidogenic activity between theca externa and interna, respectively. Numerous factors were differentially expressed in follicles of xenograft versus ovarian origin, highlighting the potential contribution of humoral factors to follicular development that have not been considered, to date. These data shed light on previously undescribed subpopulations of both GC and TC compartments and provide a systems level portrait of cellular diversification in early antral human follicles.