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Background: Population of stray dogs is significant in large cities of Nepal, such as Kathmandu. Most of stray dogs suffer a lack of basic health care. Considering the clinical relevance, the broad distribution and the lack of information of canine vector borne diseases (CVBD) in Nepal, the aim of this study was to evaluate the prevalence of different vector-borne pathogens (VBP) in stray dogs living in the metropolitan area of Kathmandu, and to assess different traits as possible risk factors. Methods: A total of 70 canine blood samples from stray dogs attended at the Kathmandu Animal Treatment Centre during August 2017 were collected on filter paper (Flinders Technology Associates (FTA) cards). Data regarding signalment, clinical signs and epidemiological characteristics were recorded for each animal. Real-time polymerase chain reaction assays were performed for Leishmania spp., Ehrlichia spp./Anaplasma spp., Babesia spp./Theileria spp. and Hepatozoon canis. Results: The overall prevalence detected was 31.43% for Hepatozoon canis, 31.43% for Anaplasma platys, 27.14% for Ehrlichia canis, 18.57% for Leishmania donovani species complex, 12.86% for isolates corresponding to Theileria spp., 12.86% for Babesia vogeli and 2.86% for B. gibsoni. A total of 81.43% of the dogs were positive to at least one of the VBP tested. Co-infections were detected in 41.43% of the dogs. Dogs positive to any of the VBP tested, and particularly to E. canis, were older than those that were negative. Conclusions: To our knowledge, this is the first molecular detection of VBP in stray dogs from Kathmandu, Nepal. The high prevalence of VBP detected highlights the need to implement a surveillance programme and control strategies for these CVBD in the population of stray dogs in this area. [ABSTRACT FROM AUTHOR]