General anesthesia can affect microcirculatory properties. However, differential effects on the microcirculation according to the anesthetic technique used during thoracoscopic surgery have not been well documented. We conducted a randomized clinical trial in which the effects of desflurane and propofol, both with remifentanil, on systemic arterial oxygenation during one-lung ventilation were compared in patients undergoing thoracoscopic surgery. As a subgroup analysis, we compared the effects of two commonly used anesthetic techniques, desflurane-remifentanil (n = 52) and propofol-remifentanil (n = 48), on tissue oxygen saturation using a vascular occlusion test in patients undergoing thoracoscopic surgery. Tissue oxygen saturation was higher in the desflurane than the propofol group (mean +/- standard deviation, 83 +/- 6 vs. 80 +/- 9, 84 +/- 6 vs. 76 +/- 10, and 87 +/- 7 vs. 77 +/- 10 % at 30 and 60 min of one-lung ventilation and at two-lung ventilation; adjusted p = 0.026, < 0.001, and < 0.001, respectively). The recovery slope during the vascular occlusion test, reflecting microvascular reperfusion adequacy, was higher in the desflurane than the propofol group during surgery (mean difference, 0.5 %/s; 95 % CI 0.0-0.9 %/s; p = 0.037). Desflurane-remifentanil anesthesia is associated with better microcirculation than propofol-remifentanil anesthesia in patients undergoing thoracoscopic surgery.