Segmental nevus depigmentosus and segmental vitiligo can be difficult to differentiate from each other. Differential diagnosis of these two diseases is important because they have significantly different prognoses and psychological effects. The purpose of this study is to identify clinical clues that may be helpful in differentiating these two diseases. We enrolled 63 patients with segmental nevus depigmentosus and 149 patients with segmental vitiligo. Sex, age of onset, sites involved, dermatomal distribution, margin of lesion and presence of poliosis were evaluated in both groups. The age of onset was less than 10 years in 96.8% of segmental nevus depigmentosus and 28.9% of segmental vitiligo cases. Trunk (36.5%) and cervical (38.1%) dermatomes were the most commonly involved in segmental nevus depigmentosus and face (67.1%) and trigeminal (64.4%) dermatomes in segmental vitiligo. The average number of dermatomes involved in truncal lesions was different in segmental nevus depigmentosus and segmental vitiligo (2.71 vs 1.62, P = 0.001). Segmental vitiligo on the face, neck and trunk appeared closer to the axis than segmental nevus depigmentosus (P < 0.001). Segmental nevus depigmentosus and segmental vitiligo showed significantly different margins (90.5% and 41.6% serrated, respectively; P < 0.001). We observed clinical differences between patients with segmental nevus depigmentosus and those with segmental vitiligo. Distribution (site, distance to axis, dermatome), vertical width, margin of lesion and presence of poliosis can be helpful in differentiating segmental nevus depigmentosus and segmental vitiligo.