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Canine visceral leishmaniasis (CVL) is caused by Leishmania infantum and is endemic in many areas of southeastern Brazil. We have hypothesized that the prevalence of infection by L. infantum in dogs housed in open-admission animal shelters is beyond the range of 3.4 - 9.6% reported among dogs domiciled in similar CVL-endemic areas. Hence, this study aimed to determine the rate of L. infantum infection among dogs maintained in shelters and to investigate the epidemiology of CVL in such environments by analyzing hematological and biochemical parameters. A total of 627 dogs from 17 different shelters across the State of Minas Gerais were screened using the Dual-Path Platform test and enzyme-linked immunosorbent assay and 211 (33.6%) were found to be seropositive in both tests. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed on skin, bone marrow and lymphoid tissues of 118 seropositive dogs with inconclusive CVL clinical diagnosis and, of these, 78 (66.1%) were PCR+ for L. infantum and 7 (5.9%) were PCR+ for L. amazonensis. One dog presented a PCR-RFLP profile that was consistent with co-infection by both parasites. Leishmania amazonensis DNA was detected in skin samples of six single-infected dogs and this constitutes a novel finding. Dogs infected only with L. amazonensis were less debilitated than those infected by L. infantum, which showed typical clinical manifestations of CVL. The co-infected dog showed only mild clinical signs. The results presented herein not only support our original hypothesis but also suggest that dogs are potential reservoirs of L. amazonensis. Public health authorities should acknowledge their responsibility towards animals in collective shelters, recognize that they are potential foci of zoonotic diseases, and establish proper functioning directives to minimize transmission to humans and to other dogs.