Ovarian follicles are complex multicellular structures that develop markedly within a dynamic tissue environment. Although cells constantly differentiate and acquire unique activities such as synthesis of steroids, during folliculogenesis, the genetic expression patterns underpinning phenotypic changes remain somewhat unknown. As a first step we compared expression of genes and consequently identified proteins among various components of bovine follicles at antral and pre-antral stages. Laser capture microdissection and Affymetrix bovine mRNA microarray analysis and Partek analysis software was used to identify gene expression in specific cells of the theca interna of pre-antral follicles, interstitial stroma and tunica albuginea (n=4 per group) as previously described (1). Gene transcripts were compared to those expressed by thecal cells from antral follicles (n = 6) collected by dissection. Genes significantly (P < 0.05) upregulated > 2-fold in the theca interna of pre-antral follicles compared to theca interna of antral follicles included MLF1IP, ACD, PLN and IL17RD. Down-regulated genes included PHLDB2, MFAP3, LGALS1, OGN, RGS5, BEX2 and LYVE1. Quantitative RT-PCR showed higher expression of GSTA3, RXFP2 and NR5A in the theca interna compared to tunica and interstium (P<0.001). In addition, RGS5 was higher in interstitial tissue in comparison to tunica (P<0.01). LGALS1, PLN, OGN, ALDH1A1 and ACD were all detected by Western immunoblot in ovary samples. PLN was more highly expressed in tunica and interstitial stroma than in the theca (P<0.01), as was OGN (P<0.0001), while ACD and LGALS1 did not differ among groups. LGALS1, OGN and PLN localised to the extracellular matrix, stromal cells and smooth muscle cells respectively, as shown by immunohistochemistry. These data are consistent with patterns of gene expression, correlated with expression of proteins, that characterise different cells within the follicles at different stages of development. Research currently underway is aimed at linking the changes in expression to cellular function.