Berberine (BR) has been proved to promote endothelial function. However, the exact mechanisms underlying the effect of BR on endothelial function are not completely clear. It has been demonstrated that endothelial progenitor cells (EPCs) contribute to improvement of endothelial function and C2 small artery elasticity index is a surrogate parameter for the clinical evaluation of endothelial function. We hypothesized that BR-induced mobilization of circulating EPCs is associated with BR-related improvement of endothelial function. To address this assumption, 15 healthy volunteers were recruited and received BR 0.4 g three times per day for 30 days. The number of circulating CD34/KDR double-positive cells as well as C1 large and C2 small artery elasticity indices were evaluated before and after BR therapy. The number of CD34/KDR double-positive EPCs increased significantly after BR treatment (0.030 ± 0.020% vs 0.017 ± 0.010%, P<0.01). After 30-day BR therapy C2 increased significantly (6.21 ± 2.80 ml per mm Hg × 100 vs 4.06 ± 2.67 ml per mm Hg 100, P<0.01) and C1 remained unchanged (10.79 ± 3.27 ml per mm Hg × 10 vs 10.06 ± 2.08 ml per mm Hg × 10, P>0.05). The increment of CD34/KDR double-positive EPCs was positively correlated with the increment of C2 (r = 0.68, P<0.01). We concluded that BR-induced mobilization of circulating EPCs contributes to improvement of small artery elasticity in healthy persons.