Follicle development is regulated by the interaction of endocrine and intrafollicular factors, as well as by numerous intracellular pathways, which involves the transcription of new genes, although not all are known. The aim of the present study was to determine the expression of a set of unknown genes identified by bovine cDNA microarray analysis in theca and granulosa cells of dominant and subordinate follicles, collected at a single stage of the first follicular wave using quantitative real-time polymerase chain reaction. Differences were further examined at three stages of the follicular wave (emergence, selection and dominance) and bioinformatics tools were used to identify these originally unknown sequences. The suggested name function and proposed role for the novel genes identified are as follows: MRPL41 and VDAC2, involved in apoptosis (dominant follicle development); TBC1D1 stimulates cell differentiation (growth associated with dominant follicle selection and development); STX7, promotes phagocytosis of cells (subordinate follicle regression); and SPC22 and EHD3, intracellular signalling (subordinate follicle regression). In conclusion, we have identified six novel genes that have not been described previously in ovarian follicles that are dynamically regulated during dominant follicle development and presumably help mediate intracellular signalling, cell differentiation, apoptosis and phagocytosis, events critical to follicular development.