In monovulatory species such as cattle, unknown mechanisms lead to the selection of one of a cohort of developing ovarian follicles to assume dominancy 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. InhibinA, apolipoproteinE receptor2 (apoER2), MAPKKK5 (ask1) and carboxypeptidaseD were isolated and verified to be reliable markers for dominant follicles (DF) using real-time RT-PCR. Before the time point where dominant follicles can be distinguished by virtue of their deviation in size and growth rate, transcripts for inhibinA, apoER and p450 aromatase were elevated specifically in the one to three largest follicles. At day 2.5 post-ovulation, near the time of dominant follicle selection, the mRNA expression profiles of MAPKKK5 and carboxypeptidaseD paralleled that of the other three genes, thus anticipating the clear molecular expression differences seen between the DF and the next largest follicle a day later. The functional relevance of elevated levels of these genes in the selection and maintenance of the dominant follicle is discussed.