Objective To explore the histopathological basis of different anatomic subunit of facial port-wine stain (PWS) treated by pulsed dye laser (PDL) and to illustrate the possible explanation for the discrepancy of therapeutic efficacy. Meth-ods Six PWS patients had biopsies and underwent PDL treatments in different anatomic subunit of facial PWS (A and B area). The diameter and depth of PWS vessels were analyzed and the clinical efficacy were evaluated by chromameter assess-ment 2 months after treatment. Results All patients were treated on both sites, according to the chromameter evaluation, av-erageΔa*and averageΔE were 4.63±2.24 and 8.81±2.24 for B area, while-0.19±2.40 and 3.55±1.46 for A area respective-ly (P<0.05). Histopthological observation showed that ectatic vessels in B area were primarily distributed in super dermis, while the ectatic vessels in A area were distributed extensively from capillaries to the reticular dermis, and even deep into the subcutaneous tissue. The Pearson correlation coefficient suggested that the depth and diameter of PWS vessels were negative-ly related to efficacy outcomes of PDL treatment. Conclusion Better results can be obtained in lateral facial PWS compared to central facial PWS on the same patient. The differences in histopathological manifestation, especially the depth of vessels, may be responsible for the discrepancy of therapeutic efficacy.