Objective To explore the postmortem stability of nine Housekeeping gene mRNA—β-actin, GAPDH, RPL32, PKG1, SDHA, rRPL13, HPRT, TBP, YWHAZ and the correlation between its relative expression and postmortem interval (PMI) in rat brain tissue and skeletal muscle. Methods 33 healty adult SD rats were randomly divided into 11 groups at 11 postmortem interval(0h, 1h, 3h, 6h, 12h, 24h, 2d, 4d, 8d, 16d, 24d), sacrificed by cervic al dislocation and it's anterior tibial muscle and brain tissue (about 50mg) were extracted, respectively. The total RNA was extracted from organizations and the nine mRNA were detected by Real-time RT-PCR. Proper internal reference was selected by geNorm software. To evaluate the stability of genes by GeNorm, NormFinder and BestKeeper software. Regression analysis by spss software. Results The expression of HPRT is the most stable in both brain and skeletal muscle, suitable for reference gene. The relative expression levels of SDHA, RPL32 and TBP in brain tissue had a certain linear relationship with PMI. While there was no significant correlation between the relative expression of RNA and PMI in skeletal muscle. Conclusion Brain tissue and skeletal muscle could be suitable materials for extracting RNA in advanced stage PMI. The relative expression levels of SDHA, RPL32 and TBP had a certain linear relationship with PMI, which could be auxiliary indices for the estimation of PMI.