It is known that hair can accumulate environmental toxics and excrete foreign chemical or biological substances. In this context, we hypothesized that foreign DNA could be found in the hair of an infected organism, and thus, be detected by Real Time PCR in the hair of Leishmania infantum naturally infected dogs. A population of 28 dogs living in Leishmania endemic areas was divided into two groups: A (13 Leishmania infected dogs) and B (15 healthy dogs). Blood, lymph node and ear hair samples from all of them were tested for the presence of parasite kinetoplast DNA (kDNA). For the same purpose, hair of several body areas and hair sections of two infected dogs were also analyzed. Epidermal keratinocytes from an infected animal were also analyzed for reactivity against Leishmania antigens by ELISA and for the presence of kDNA. Regarding to dogs from group A, parasite kDNA was detected in the 100% of lymph node samples. The sensitivity of Real Time PCR in ear hair was similar to that obtained in blood (9 positive out of 13 versus 8 positive out of 13, respectively). Moreover, the presence of L. infantum kDNA was also detected in the hair of all the analyzed body zones, in all hair sections and in epidermal keratinocytes. In infected dogs, parasite kDNA could be detected and quantified from just one single hair, whereas it was not detected in any of the samples of the healthy dogs. This work describes a new method for a reliable and non-invasive diagnosis of canine leishmaniosis using hair samples of infected animals. The data presented also provide some insights for the understanding of the physiology of keratinocytes and the role of hair as a specialized tissue in the kidnapping and removal of foreign DNA.