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Vitiligo and halo nevi are both pigmentary disorders of the skin characterized by the acquired loss of functional epidermal melanocytes manifesting as white macules and patches. The cellular mechanism(s) and biochemical changes that result in the appearance of these two types of achromic lesions are still uncertain; and the relationship between vitiligo and halo nevi has been in dispute. In this study, we investigated the ultrastructure of mitochondria in melanocytes and in keratinocytes from perilesional vitiligo skin and from perilesional halo nevi skin using Transmission Electron Microscopy. Furthermore, we performed a quantitative analysis of mitochondrial morphology through a stereological study. As previously reported, we found that melanocytes from perilesional active vitiligo skin were loosely connected with their surroundings by their retracted dendrites. The surface density and the volume density of mitochondria in melanocytes and in keratinocytes from perilesional vitiligo skin are increased significantly compared with the controls, especially in active vitiligo. In contrast, there are no significant differences in mitochondria in melanocytes and in keratinocytes from perilesional halo nevi skin compared with the controls. In summary, the tendency of different morphologic alterations in mitochondria from perilesional vitiligo skin and from perilesional halo nevi skin reflect heterogeneous backgrounds between the two diseases, revealing that vitiligo and halo nevi may have separate pathogenic mechanisms. These findings may help elucidate the relationship of these two diseases and their underlying mechanisms.