Prior to the development of high-throughput methods for the analysis of differential gene expression, genes required for proper ovarian function were identified on a case-by-case basis. Recently, however, several techniques have been developed that enable investigators to study large-scale changes in gene expression under a variety of experimental conditions. The utilization of these methodologies has led to the identification of a number of novel or previously unappreciated genes that are expressed within distinct cell types in the ovary or at specific stages of the ovarian cycle. This review details the recent use of differential analysis strategies in identifying (i) genes that are expressed exclusively or preferentially in the ovary, (ii) genes that are differentially expressed in isolated ovarian cells in response to hormonal stimulation, and (iii) those genes that are expressed at specific stages of the ovarian cycle. The genes identified through the use of these approaches represent potential targets for designing agents capable of regulating ovarian physiology and thus fertility.