The inability to obtain in vivo samples of antral follicle wall layers without removing the ovaries or sacrificing the animals has limited more in-depth studies on folliculogenesis. In this study, a novel ultrasound-guided follicle wall biopsy (FWB) technique was used to obtain in vivo follicle wall layers and follicular fluid samples of growing antral follicles. The expression of proliferative, hormonal, angiogenic, and pro-/antiapoptotic receptors and proteins in the follicular wall among three follicle classes were compared during the spring transitional anovulatory (SAN) and spring ovulatory (SOV) seasons in mares. The main findings observed in the granulosa, theca interna, and/or all follicle layers during the SOV season compared with the SAN season were (a) small-sized follicles (10-14 mm) had greater epidermal growth factor receptor (EGFR) and Bcl-2 expression; (b) medium-sized follicles during the expected deviation/selection diameter (20-24 mm) had greater expression of EGFR, Ki-67, luteinizing hormone receptor (LHR), and Bcl-2; and (c) dominant follicles (30-34 mm) had greater EGFR, Ki-67, vascular endothelial growth factor, LHR, and Bcl-2 expression. Estradiol related receptor alpha expression and intrafollicular estradiol concentration increased, along with an increase in follicle diameter in both seasons. In this study, the application of the FWB technique allowed a direct comparison of different receptors' expression among follicles in different stages of development and between two seasons using the same individuals, without jeopardizing their ovarian function. The successful utilization of the FWB technique and the mare as an experimental animal offer a great combination for future folliculogenesis studies on mechanisms of follicle selection, development, and ovulation in different species, including women.