Understanding of gene expression and metabolic, biological, and physiological pathways in ovarian follicular development can have a significant impact on our understanding of the dynamics of follicular atresia or survival. In fact, some oocyte loss occurs during the transition from secondary to early tertiary follicles. This study aimed to understand, by microarray analysis, the temporal changes in transcriptional profiles of secondary and early antral (tertiary) follicles in caprine ovaries. Ovarian follicles were microdissected and pooled to extract total RNA. The RNA was cross-hybridized with the bovine array. Among 23 987 bovine genes, a total of 14 323 genes were hybridized with goat mRNAs while 9664 genes were not. Of all the hybridized genes, 2466 were stage-specific up- and down-regulated in the transition from secondary to early tertiary follicles. Gene expression profiles showed that three major metabolic pathways (lipid metabolism, cell death, and hematological system) were significantly differentiated between the two follicle stages. In conclusion, this study has identified important genes and pathways that may potentially be involved in the transition from secondary to early tertiary follicles in goats.