It is well established that endocrine-disrupting chemical (EDC) exposures during early development can cause ovarian dysfunction by adulthood. Studies with the organochlorine pesticide methoxychlor (MXC), a model EDC with estrogenic and anti-estrogenic activities, have demonstrated that neonatal and fetal exposure [embryonic day 18 to postnatal day (PND) 7] lead to accelerated puberty, irregular estrus cycles, reduced litter sizes, reduced superovulatory response to gonadotropins, and premature reproductive aging. In PND 50-60 ovaries, there was a disruption of follicular progression with a large number of follicles found in the early antral follicle stage with a concomitant reduction in corpora lutea. Furthermore, immunohistochemical studies showed that MXC-treated ovaries had decreased levels of CYP11A1 and LHR proteins in mid-late antral follicle stages and reduced ESR2 expression in the preantral and early antral follicles. Interestingly, there was no significant effect on ESR2 expression at earlier follicular stages such as primary and secondary follicles. Other studies with granulosa cell (GC) cultures demonstrated an enhanced effect of HPTE (a major metabolite of MXC) only in cells stimulated with FSH suggesting that gonadotropin responsive stages of follicles/GCs were more likely to exhibit the MXC mediated detrimental effects. Therefore, to identify the specific stages and the molecular/epigenetic mechanisms involved in EDC-associated effects, follicular isolations were performed. The objectives were (1) to establish a robust follicle separation method by enzymatic digestion and (2) to compare the gene expression patterns at the various follicular stages. Enzymatic digestions were performed with Collagenase Type I and various size beads (Polysciences, Inc.) were utilized to categorize the follicles into three groups: (1) “small” (50-180 μm, up to and including early pre-antral), (2) “medium” (180-300 μm, late pre-antral and early antral), and (3) “large” (300-700, mid- and late-antral follicles. Granulosa cells were collected from the large follicles by puncturing them prior to the enzymatic digestion. In this manner, approximately 25-30 small, 10-20 medium follicles and ~6 x 10-5 GCs from large follicles, per rat (n = 3), were obtained and RNA was isolated. Gene expression analyses were conducted after whole transcriptome amplification and QPCR with Taqman assays. Small follicles had a 100- to 200-fold enrichment ( p < 0.001) of Gdf9 and Bmp15 transcripts while GC from the large follicles had an enrichment of 100- to 500-fold ( p < 0.001) in steroidogenic enzyme transcripts such as Cyp11a1, Cyp19a1, and Hsd17b1 . These data validated our isolation techniques. Currently these data are being compared to those obtained from laser capture microdissection technique. Together they provide a useful tool for future studies of EDC exposed ovaries wherein gonadotropin responsive follicular stage-dependent gene expression and epigenetic analyses can be performed. Supported by R56 ES017059 from NIEHS (MU) and TUBITAK– BIDEB 2219 International Postdoctoral Fellowship Program (KA).