Abstract: Objective To select the internal control genes in gene expression study before and after hypothermal cardiopulmonary bypass（CPB）. Methods Eleven human housekeeping genes（HKGs） were included in this study,and the primer pairs for their amplification were designed by Beacon Designer software. Venous blood samples were collected from 4 patients before CPB,at minimum body temperature,at end of CPB,and days 1,3 and 7 after CPB. After total RNA was extracted from blood samples,mRNAs were measured by SYBR Green I based real-time fluorescent quantitative RT-PCR and cycle threshold values were acquired. Finally,average expression stability value of the remaining HKGs and the optimal number of internal control genes for normalization were calculated and determined according to the cycle threshold values by geNorm VBA applet. Results The 11 HKGs according to their expression stability were UBC,RPLP0,PGK1,18S-rRNA,PPIA,GAPDH,ACTB,TBP,B2M and EEF1A1/HPRT1 in order. The last three genes were the optimal internal control genes for the research. Conclusion Three most stable genes,EEF1A1,HPRT1 and B2M,can be chosen as optimal internal control genes in gene expression study before and after hypothermal cardiopulmonary bypass.