In monoovulatory species such as cattle, unknown mechanisms lead to the selection of one of a cohort of developing ovarian follicles to assume dominance and continue to grow in each follicular wave. We have used suppressive subtraction hybridization to identify genes differentially expressed in the granulosa cells of dominant and subordinate follicles. Inhibin beta A, apolipoprotein E receptor 2, MAPK kinase kinase 5 (ask1), and carboxypeptidase D were isolated and verified to be reliable markers for dominant follicles using real-time RT-PCR. Before the time point at which dominant follicles can be distinguished by virtue of their deviation in size and growth rate, transcripts for inhibin beta A, apolipoprotein E receptor 2, and p450 aromatase were elevated specifically in the one to three largest follicles. On d 2.5 postovulation, near the time of dominant follicle selection, the mRNA expression profiles of MAPK kinase kinase 5 and carboxypeptidase D paralleled those of the other three genes, thus anticipating the clear molecular expression differences seen between the dominant follicle and the next largest follicle 1 d later. The functional relevance of elevated levels of these genes in the selection and maintenance of the dominant follicle is discussed.