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Background: We evaluated kDNA PCR/hybridization and quantitative real-time PCR (qPCR) targeting the gene of DNA polymerase of Leishmania infantum for CVL diagnosis and assessment of parasite load in clinical samples obtained invasively and non-invasively. Methodology/Principal Findings: Eighty naturally infected dogs from an endemic urban area in Brazil were used. Animals were divided into two groups based on the presence or absence of CVL clinical sings. Skin biopsies, bone marrow, blood and conjunctival swabs samples were collected and submitted to L. infantum DNA detection. In addition, anti-Leishmania antibody titers were measured by Immunofluorescence antibody test. The symptomatic dogs had increased titers compared to asymptomatic dogs (P = 0.025). The frequencies of positive results obtained by kDNA PCR/hybridization for asymptomatic and symptomatic dogs, respectively, were as follows: right conjunctiva, 77.5% and 95.0%; left conjunctiva, 75.0% and 87.5%; skin, 45.0% and 75.0%; bone marrow, 50.0% and 77.5%; and blood, 27.5% and 22.5%. In both groups, the parasite load in the skin samples was the highest (P<0.0001). The parasite loads in the conjunctival swab and bone marrow samples were statistically equivalent within each group. The parasite burden in conjunctival swabs was higher in the dogs with clinical signs than in asymptomatic dogs (P = 0.028). This same relationship was also observed in the bone marrow samples (P = 0.002). No differences in amastigotes load in the skin were detected between the groups. Conclusions: The conjunctival swab is a suitable clinical sample for qualitative molecular diagnosis of CVL. The highest parasite burdens were detected in skin regardless of the presence of VL-associated clinical signs. The qPCR results emphasized the role of dogs, particularly asymptomatic dogs, as reservoirs for CVL because of the high cutaneous parasite loads. These results may help to explain the maintenance of high transmission rates and numbers of CVL cases in endemic urban regions. Author Summary: Visceral leishmaniasis (VL) is considered the most lethal manifestation among the diseases caused by genus Leishmania. The main control measures for VL are: diagnosis and early treatment of human cases, insecticide vector control, and euthanasia of seropositive dogs. Although these strategies have been continuously applied in Brazil, the number of VL cases has increased and this disease still poses as a serious public health problem. Belo Horizonte is an endemic urban area in Brazil and it is considered by the Ministry of Health the third most affected Brazilian metropolitan region by VL. In the context of prophylaxis, the correct diagnosis of infected dogs is critical for the VL control because dogs represent the main domestic reservoir. However, the serological diagnosis techniques used in large-scale for canine screening in Brazil have important limitations including the difficulty of diagnosing asymptomatic dogs. Molecular methods based on Polymerase Chain Reaction (PCR) and real-time PCR (qPCR) have greatly improved VL diagnosis. Based on this, we aimed to evaluate different canine clinical samples for qualitative VL diagnosis by PCR and quantification of parasite load by qPCR in dogs from Belo Horizonte. The possible implications of results are discussed with emphasis on skin and conjunctival swab samples. [ABSTRACT FROM AUTHOR]