Objective To study the expression of polycystin1 and polycystin2 in dissection aorta specimens by Real time PCR and immunohistochemisty. Methods Twelve descending dissection aorta specimens from patients of acute Stanford B dissection were taken during surgery; 12 normal descending aorta specimens were taken from multi-organ donors. The G APDH gene was used as control, gene expression of polycystinl and polycystin2 were compared in these two groups with Real time PCR. The expression of polycystinl and polycystin2 protein were showed with immunohistochemisty in the specimen of these two groups. Three high magnify fields were randomly chosen to count the expression of polycystin1 and polycystin2 protein. The counting of polycystin1 and polycystin2 protein were compared between these two groups. Results The gene expression of polycystinl in AD group is 0. 32 fold as that in the control group (P ＜ 0.01 ) and polyeystin2 in AD group is 0.34 fold as that in the control group (P ＜0.01 ); The protein expression of polyeystinl was 0.47 folds as that in the control group ( P ＜ 0.05 ) and polycystin2 in AD group is 0.35 folds as that in the control group ( P ＜ 0.01 ). Conclusions The expression of polycystin1 and polycystin2 on gene and protein level were down regulated in AD group. The down regulation of polycystinl and polycystin2 may play a pivotal role in the development of AD.