Immunoproteomics using sera of women with ovarian autoimmune diseases such as primary ovarian insufficiency and IVF embryo transfer recruits led to identification of three proteins namely alpha actinin 4 (a-ACTN4), heat-shock 70 protein 5 (HSPA5), and actin beta (ACTB). This study deals with the establishment of a peptide ELISA for screening sera of antiovarian antibody (AOA)-positive patients and further delves into understanding the role of these three proteins in ovarian autoimmunity in a mouse model. Using in silico approach, antigenic peptides of these proteins were identified and used for peptide ELISA. ELISA results indicated that AOA-positive sera showed reactivity with only specific peptides. The functional significance of the dominant peptides was studied by active immunization of female mice with these peptides. All immunized mice generated high antibody titers and profound effect on ovaries with few primordial (2.4G0.1, 2.4G0.2, and 2G0.1), primary (2.4G0.5, 1.7G0.3, and 2.4G0.3), preantral (2.3G0.5, 3.4G0.3, and 2.9G0.3), antral (0.9G0.2, 1.6G0.8, and 2.3G0.6) follicles, and corpora lutea (2.8G0.8, 2.9G1.7, and 4.6G2.3), and increased number of atretic follicles (5.5G0.4, 4.9G1.8, and 7.5G1.0) in ACTN4-, HSPA5-, and ACTB-immunized mice compared with control animals (3.0G0.2, 3.5G0.6, 3G0.1, 3.6G0.2, 4.7G0.3, and 1.5G0.3) respectively. These mice when mated with fertile male mice showed an overall 25-43% reduction in fertility compared with controls. The data clearly suggest that the dominant antigenic epitopes of the three proteins play critical role in fertility and could possibly be the key autoimmune targets. These epitopes could be used to develop a more specific and sensitive diagnostic test for women with ovarian autoimmune diseases and to design therapy for disease management for reinstatement of ovarian function.