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A unique index line of pigs created by long-term selection ovulates on average 6.7 more ova than its randomly selected control line. Expression profiling experiments were conducted to identify differentially expressed genes in ovarian tissues of the index and control lines during days 2–6 of the follicular phase of the estrous cycle. Fluorescently labeled cDNAs derived from ovary and follicle RNA were cohybridized on microarray slides (n = 90) containing 4608 follicle-derived probes printed in duplicate. Statistical analysis of the resulting ~1.6 million data points with a mixed-model approach identified 88 and 74 unique probes, representing 71 and 59 unique genes, which are differentially expressed between lines in the ovary and ovarian follicles of different size classes, respectively. These findings indicate that long-term selection for components of litter size has caused significant changes in physiological control of the dynamics of follicular maturation. Genes involved with steroid synthesis, tissue remodeling, and apoptosis, in addition to several genes not previously associated with ovarian physiology or with unknown function, were found to be differentially expressed between lines. This study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the quantitative genetic control of reproduction.