Background: The clinical application of flow-through anastomosis has been reported in various studies; however, no studies have quantitatively evaluated and compared the actual hemodynamics in flow-through anastomosis and end-to-end anastomosis. This study quantitatively evaluated the blood inflow (volumetric flow rate) and vascular resistance (pulsatility index) of flow-through arterial anastomosis using an ultrasonic flowmeter, and compared these values with those of end-to-end anastomosis in actual clinical settings. In addition, factors affecting the outcomes have also been examined. Methods: Twenty-eight patients who underwent free flap reconstruction after tumor resection were subjected to flow-through arterial anastomosis and flow examination. First, in the end-to-end state, the proximal anastomotic site was measured. This was followed by the opening of the distal arterial clamp, and measurement was then continued (in the flow-through state). Results: In flow-through arterial anastomosis compared with end-to-end anastomosis, the volumetric flow rate was significantly increased (18.9 +/- 14.1 ml/minute versus 6.0 +/- 6.3 ml/minute) and the pulsatility index was significantly decreased (5.2 +/- 3.7 versus 13.6 +/- 10.2), when comparing paired data. Multiple regression analyses revealed that a perforator flap (versus a musculocutaneous flap) was independently associated with both reduced volumetric flow rate and increased pulsatility index in end-to-end anastomosis, and that hypertension was independently associated with an increased pulsatility index in end-to-end anastomosis. However, no factors in flow-through anastomosis were significantly associated with those values. Conclusion: In terms of blood flow and vascular resistance, flow-through arterial anastomosis was considered to have promising quantitative effects and should be performed when the conditions of both the donor and recipient vessels meet the requirements.