SD rats were applied as experiment materials to screen differentially expressed genes of the uterus in different stage of pregnancy by suppression subtractive hybridization (SSH), in which the uterus from the 5th and the 19th day in pregnancy were respectively used as driver and tester. Seventy positive clones from forward subtractive library are selected by differential screening. Sequencing analysis and homology comparison showed that all these clones are homologous to eight known genes in GenBank by the degree from 90% to 100%. These genes are differentially expressed in the uterus from the 19th day in pregnancy, in which the expression of uroguanylin and interferon-inducible protein 16 in the uterus in pregnancy are reported for the first time. Semi-quantitative analysis showed that the expression of uroguanylin was significantly higher in the uterus of 19th day in pregnancy than that of 5th day (P < 0.001), however, there was no difference about the expression of interferon-inducible protein 16. The expression of uroguanylin increased after embryo implantation, decreased on the 15th day and reached the peak on the 19th day in pregnancy. The result suggested that uroguanylin might be concerned with parturition.