The aim of this study was to examine the expression and regulation of peroxisome proliferator-activated receptor delta (PPAR) gene in rat uterus during early pregnancy by in situ hybridization and immunohistochemistry. PPAR mRNA expression in the luminal epithelium was high on day 1 of pregnancy, gradually declined from day 2 and was undetectable on day 5 of pregnancy. However, expression in the glandular epithelium began to increase from day 2 and was high on day 5 of pregnancy. There was no detectable PPAR immunostaining in the luminal and glandular epithelium from day 1 to day 5. On day 6 of pregnancy when embryos implanted, PPAR mRNA and immunostaining were intense in the subluminal stroma at implantation sites. On days 7 and 8, there was strong expression of both PPAR mRNA and intense immunostaining in the decidualized area near the lumen. There was low expression of PPAR in the subluminal stroma and glandular epithelium under delayed implantation. After delayed implantation was terminated by oestrogen treatment and embryo implantation was initiated, both PPAR mRNA and immunostaining were strongly induced in the subluminal stroma. Intense PPAR immunostaining was observed in the decidua under artificial decidualization, while no detectable immunostaining was seen in the uninjected control horn. Retinoid X receptor (RXR) immunostaining was seen in the subluminal stroma surrounding the implanting blastocyst on day 6 and in the decidual cells on days 7 and 8 of pregnancy. In conclusion, the high PPAR expression at implantation sites and in the decidual cells in rat uterus indicates that PPAR may play an important role during implantation and decidualization.