Bovine gammaherpesvirus 6 (BoGHV6), formerly known as bovine lymphotropic virus, belongs to the genus Macavirus, which includes the porcine lymphotropic herpesviruses (PLHV) and members collectively referred to as malignant catarrhal fever virus (MVFV) group. This study investigated the possible participation of BoGHV6 in the development of intestinal and pulmonary diseases of buffaloes. Intestinal and pulmonary fragments were obtained from 19 buffaloes from Goiás, Central-western Brazil. Histopathology revealed interstitial pneumonia in all pulmonary fragments evaluated, while two of these had suppurative bronchopneumonia. Furthermore, all intestinal fragments demonstrated atrophic enteritis. BoGHV6 DNA was amplified from 31.6% (6/19) of the buffaloes with interstitial pneumonia and in 26.3% (5/19) with atrophic enteritis. The phylogenetic evaluation revealed that the strain of BoGHV6 amplified from these buffaloes had 100% nucleotide (nt) sequence identity with the reference strains of BoGHV6, but only 69.5 to 73.7% and 65.8 – 69.5% nt sequence identity with members of the MCFV and the PLHV, respectively. Additionally, molecular assays to detect important pathogens of ruminants did not amplify the respective nucleic acids in the tissues evaluated. These results demonstrated that BoGHV6 was amplified from tissues of buffaloes with histopathologic diagnoses of interstitial pneumonia and atrophic enteritis, suggesting the possible participation of this virus in the development of the intestinal and pulmonary lesions herein identified.