In South America, visceral leishmaniasis is a zoonotic disease with severe evolution characteristics in humans, and dogs are its main reservoir. In this context, this study aimed to evaluate the clinical status of dogs from a Brazilian endemic area naturally, at Barra Mansa municipality, infected with Leishmania infantum, in conjunction with their histopathological profile and, in order to determine possible markers of susceptibility or resistance to the disease, parasitic DNA load, cytokine and iNOS mRNA expression profiles were investigated in lymph nodes. High levels of IFN-ɣ and IL-6 mRNA were detected. Both IFN-ɣ and IL-6 mRNA were associated with disorganization of the corticomedullary region. IFN-ɣ and TNF-α mRNA were associated with the absence of follicular hyperplasia. The regulatory pathway was remarkable with IL-10 mRNA detection and its significant association with the severity of the disease. Plasmacytosis and sinus histiocytosis were associated with high loads of parasitic DNA, but there was no significant association between the parasite DNA load and animal clinical alterations. Since high parasitic loads were found in animals with or without symptoms, clinical examination cannot be considered as a criterion for disease susceptibility assessment.