Objectives To evaluate histological and immunohistochemical changes in the great saphenous vein after endovenous laser ablation at two different wavelengths (1470 vs. 1940 nm) and linear endovenous energy density values (50 vs. 100 J/cm). Method Segments were obtained from the conventional eversion removal of great saphenous vein and divided into a control group and four groups for ex vivo irradiation (control group; A: 1470 nm, 50 J/cm; B: 1470 nm, 100 J/cm; C: 1940 nm, 50 J/cm; D: 1940 nm, 100 J/cm). Fifty venous segments ( n = 10/group) were analyzed. Changes were classified into low-temperature changes, moderate-temperature changes, high-temperature changes, and very high-temperature changes. Results In the intima, low-temperature changes + moderate-temperature changes were significantly more prevalent in group A (65.4%) than in D ( p = 0.001). In the media, low-temperature changes + moderate-temperature changes were achieved mostly in groups A and C (77.4% and 75.0%, respectively). In adventitia fragments, 100% of changes in group A were low-temperature changes + moderate-temperature changes. Conclusions The 1940-nm laser wavelength with linear endovenous energy density of 100 J/cm was excessively destructive to the intima and media causing a high rate of high-grade thermal damage. These findings corroborate the possibility of using lower linear endovenous energy densities with 1940-nm devices to achieve effective occlusion with less high grade thermal damage to the intima and media, as well as to prevent damages to the adventitia and perivenous tissues, including venous perforation and its attendant clinical consequences.