Objective To investigate the correlation between the polymorphism of 5-HTT gene-linked polymorphic region（ 5-HTTLPR） gene and cognitive impairment in the patients with bipolar disorder（ BPD）. Methods The technique of polymerase chain reaction-restriction fragment length polymorphism（ PCR-RFLP） was applied to identify the genotypes for the polymophism of 5-HTTLPR gene in 100 patients with BPD and 100 healthy subjects. We assessed cognitive function of the subjects by event related potentia（ ERP）. Hamilton Rating Scale for Depression（ HAMD） and Bech-Rafaelsen Mania Rating Scale（ BRMS） were respectively used to determine the severity of depressive and manic phase for the BPD patients. Results The frequency of 5-HTTLPR genotypes and allelic gene were mot significantly different between BPD patients and healthy subjects（ P ＞ 0.05）. The BRMS scores of manic phase were significantly associated with the latency of ERP P3（ r=0.321， P＜ 0.01）. The HAMD scores of depressive phase were significantly associated with the latency and amplitude of ERP N1， ERP N2， ERP N3 and ERP P3（ r=0.637， 0.379， 0.472， 0.572， 0.433； P＜0.05）. Compared to patients with SS genotype， patients carrying LL gneotype were tend to have manic phase（ OR=2.471，P＜0.05）. The comprehensive analysis of disordered multi classification Logistic regression models showed that only the P3 amplitude of manic phase entered the regression equation（ P=0.033）， and the remaining variables did not enter. Conclusions The polymophism of 5-HTTLPR gene is not associated with BPD risk and ERP. Impairment of cognitive function occurs in all patients with bipolar disorder. The patients with depressive phase have more damage of cognitive function， and compared to SS genotype， the BPD patients carrying LL genotype are inclined to get manic phase.