Immune-compromised mice have been used as gonadal tissue recipients to develop gametes of various mammalian species. The aim of this research was to determine gene expression differences between fresh and frozen-thawed rat xenotransplanted (XT) ovaries as well the gene expression differences between XT and sexually mature rat ovaries that were non-transplanted (NT). Ovaries from sexually immature female rats were transplanted under the kidney capsule of ovariectomized athymic nude mice either fresh or after freezing. The XT ovaries were collected approximately 10-12 weeks after xenografting for microarray analysis. The NT ovaries were collected from sexually mature rats. Gene expression was very similar between fresh and cryopreserved XT ovaries: 125 genes were twofold up- or downregulated, but level of regulation was not statistically significant. Overall patterns of gene expression between XT and NT ovaries were very different indicated by the absence of diagonal relationship between XT and NT ovary gene expression. More than 3000 genes were significantly (P<0.01) up- or downregulated between XT and NT ovaries. Genes involved in metabolic processes, lipid metabolism, and growth were downregulated in XT ovaries, whereas genes involved in immune and inflammatory response were upregulated in XT ovaries. The results showed that ovarian tissue xenografting significantly alters genes responsible for ovarian metabolism and function and leads to an upregulation of genes responsible for graft rejection.