To investigate the relationship between hypoxia and epididymal dysfunction and the mechanism of epididymal dysfunction in rats with left-side varicocele, a total of 45 male Wistar rats were randomly divided into three groups in average. The expression of hypoxia-inducible factor-1α (HIF-1α) was detected by Western blot and immunohistochemical analysis respectively. HIF-1α was expressed in the experimental group, and the positive rate was significantly higher than that of either the sham or the control group (P < 0.05). The apoptosis index (AI) of epididymal epithelium was higher in the experimental group (7.25 ± 2.56) than that in either the sham (0.52 ± 0.57, P < 0.01) or the control group (0.08 ± 0.13, P < 0.01). Additionally, the levels of sialic acid and carnitine were lower in the experimental group than that in either the sham or the control group (P < 0.05) and were significantly negatively correlated with HIF-1α expression (r = -0.620, P = 0.014, and r = -0.610, P = 0.016 respectively). It is concluded that left-side varicocele could cause epididymal hypoxia and epididymal dysfunction. Moreover, HIF-1α maybe act as useful factor to predict germ cell apoptosis in varicocele.