Background: We have characterized a new variant of endemic pemphigus foliaceus in El Bagre (El Bagre-EPF) (AKA pemphigus Abreu-Manu) and surrounding municipalities. Herein, we describe nail alterations in several patients affected by this disease. In the pre-steroid era, patients with endemic pemphigus foliaceus (EPF), especially in Brazil where the disease is known as fogo selvagem (FS), were described to have some nails changes including the Viera's sign (yellowish of the nail). In this study, we have attempted to describe a range of nail alterations in patients affected by El Bagre-EPF. Methods: A case-controlled study was conducted where 40 cases and 40 controls were evaluated for nail changes. A clinical exam was performed in the cases and in a series of control patients from the same geographic region who were matched by age, gender and work activities. Gram stains and cells cultures for fungus and bacteria were done on affected nails. Results: In 25 chronic patients (affected for more than two decades) presented with toenail alterations. These changes included change of color nail (yellowish) (Viera sign), atrophy, dystrophy, chronic paronychia, onycholysis, nail bed erosion, subungual hyperkeratosis and trachyonychia. All of these findings were overrepresented in patients compared with control population (p < 0.05). Cell cultures and gram stains were negative in all study participants. Discussion: Chronic patients have nail damage, maybe due to the presence of chronic inflammatory process affecting the nail bed cell, matrix, and/or the nail fold cells junctions.