Gentian violet ink is used as a skin marker in various surgical procedures, including neurosurgery. The dye is also used to visualize the edges of blood vessels during bypass surgery. However, gentian violet ink carries the risks of carcinogenicity and venous injury, which causes microvascular thrombosis. Objective The objective of this study was to compare the gentian violet-free dye C.I. Basic Violet 4 (BV4) and gentian violet. The usefulness, in terms of color, and the formation of microvascular thrombosis in anastomosis were compared. Methods We used the gentian violet-free dye in 20 cases involving 3 vascular anastomoses. The bone cutting lines on the bone surface, superior temporal artery, and middle cerebral artery were drawn using BV4 and gentian violet ink. Results The colors of BV4 and gentian violet ink were similar. No thrombus formation was observed at the vascular anastomosis when using BV4. Conclusion BV4 can be used similarly to gentian violet ink. No adverse effects such as thrombus formation in microvascular anastomosis were experienced using BV4.