Visceral leishmaniasis is associated with a variety of hematological abnormalities. In this study, we correlated the hematological changes in the peripheral blood of dogs naturally infected with Leishmania infantum (L. infantum) with the distribution of cell lineages and cytokine gene expression patterns in the bone marrow. Samples from 63 naturally semidomiciled dogs living in an endemic area of visceral leishmaniasis were analyzed. L. infantum infection was detected in 50 dogs (79.3%). Among those, 18 (32%) had positive splenic cultures and showed more clinical signs. They also had lower red blood cell counts and leukocytosis with an increased number of neutrophils and monocytes in peripheral blood compared to dogs negative to this test. L. infantum DNA was detected in the bone marrow of 8/14 dogs with positive splenic culture. Dogs with L. infantum infection in the bone marrow presented with histiocytosis (p = 0.0046), fewer erythroid cell clusters (p = 0.0127) and increased gene expression levels of IFN-γ (p = 0.0015) and TNF (p = 0.0091). The data shown herein suggest that inflammatory and cytokine gene expression changes in bone marrow may contribute to the peripheral blood hematological changes observed in visceral leishmaniasis.