The objective of this study was to evaluate the development of preantral follicles from the Nelore breed of Bos indicus after in vitro culture of ovarian cortices in different concentrations of indole acetic acid (IAA). In addition, this study investigated the possible association of mammalian genes with IAA activity in bovine preantral follicles using an in silico approach. Ovaries (n = 8) from Nelore heifers were collected, and the ovarian cortex was divided into 14 fragments. From these samples, two fragments were immediately fixed in Carnoy solution (control), and the other fragments were cultured individually for two or six days in Minimum Essential Medium (MEM) with 0, 10, 40, 100, 500 or 1000 ng/ml of IAA. Follicles were classified as primordial or as developing (primary and secondary) follicles. The in silico approach to search for auxinresponsive candidate genes was performed with bioinformatics tools, such as GenBank and SWISS-PROT database, Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Clustal W program. Compared to the control culture, the percentage of primordial follicles was reduced (P < 0.05) and the percentage of developing follicles was increased (P < 0.05) after 2 or 6 days of culture in all media tested. Furthermore, culture of the ovarian cortex for 6 days reduced the percentage of healthy, morphologically normal follicles when compared with the control (P < 0.05). In contrast, cultures supplemented with 10 ng/ml of IAA were the only samples that had similar (P > 0.05) percentages relative to the control group. Finally, we found a mammalian gene that was homologous to the plant gene, ROOTY, which may be involved in the oocyte response to IAA. We conclude that the 10 ng/ml concentration of IAA promoted follicular survival and activation of Nelore bovine preantral follicles after 6 days of culture in vitro.