Background Cerebral venous sinus thrombosis (CVST) is a special form of stroke with multiple causes and risk factors. However, there are still a portion of cases with unknown reasons. The aim of this study was to investigate the relationship between internal jugular vein (IJV) abnormalities and the development of CVST. Methods A total of 51 CVST patients and 30 healthy controls were enrolled. The diameter, the maximum velocity (Vmax) and the reflux time in bilateral IJVs were measured by color Doppler flow imaging (CDFI). The paired t test was used to compare the numeric values between the bilateral IJVs. The Pearson chi-square test was used to evaluate the relationship between IJV abnormality and CVST, IJV abnormality and IJV reflux, respectively. Results Among the 51 CVST patients, 20 (39%) patients were with normal IJV and 31 (61%) patients were with abnormal IJV. The types of IJV abnormality included annulus stenosis 19 cases (61%), hypoplasia 9 cases (29%), thrombosis 2 cases (7%) and anomalous valve 1 case (3%). In patients with unilateral IJV abnormality, the minimum diameter of the IJV on the lesion side was significantly smaller than that of the contralateral side (P<0.0001). When compared with contralateral side, the Vmax of the lesion side with unilateral annulus stenosis was significant higher, however, it was obvious lower in patients with unilateral hypoplasia (P<0.05). Furthermore, among 27 cases with unilateral IJV abnormality, all the CVST occurred on the same side as the IJV lesions. Conclusion IJV abnormality closely correlated with the development of CVST, which is a newly identified risk factor for CVST. Chin Med J 2012;125(20):3671-3674