Infection by Rhodococcus equi is considered one of the major health concerns for foals worldwide. In order to better understand the disease’s clinical and pathological features, we studied twenty cases of natural infection by R. equi in foals. These cases are characterized according to their clinical and pathological findings and immunohistochemical aspects. Necropsy, histologic examination, bacterial culture, R. equi and Pneumocystis spp. immunohistochemistry were performed. The foals had a mean age of 60 days and presented respiratory signs (11/20), hyperthermia (10/20), articular swelling (6/20), prostration (4/20), locomotor impairment (3/20) and diarrhea (3/20), among others. The main lesions were of pyogranulomatous pneumonia, seen in 19 foals, accompanied or not by pyogranulomatous lymphadenitis (10/20) and pyogranulomatous and ulcerative enterocolitis (5/20). Pyogranulomatous osteomyelitis was seen in 3 foals, one of which did not have pulmonary involvement. There was lymphoplasmacytic (4/20), lymphoplasmacytic and neutrophilic (1/20) or pyogranulomatous arthritis (1/20), affecting multiple or singular joints. Immunohistochemistry revealed to be a valuable tool for the detection of R. equi, confirming the diagnosis in all cases. Furthermore, pulmonary immunostaining for Pneumocystis spp. demonstrates that a coinfection with R. equi and this fungal agent is a common event in foals, seen in 13 cases.