We report a case of a middle-age male patient, with newly HIV infection in AIDS stage diagnosis, no comorbitidies, who was hospitalized for subacute malaise, fever, self-limited unproductive cough and no bloody chronic diarrea. The diagnosis of Pneumocystis jiroveci pneumonia was performed by imagenological suspicion and stains of cysts of this pathogen with bronchoalveolar lavage samples. Treatment was initiated with oral cotrimoxazole and starting HAART with good clinical outcome. Concomitantly, an etiologic study was conducted for chronic diarrhea and through histopathological examination of colonic mucosa, numerous extracellular cystic structures Pneumocystis characteristics were observed, performing the diagnosis of extrapulmonary pneumocystosis. Extrapulmonary pneumocystosis is a rare cause of P. jiroveci infection, requires a high index of suspicion and should be approached in HIV patients with severe AIDS which is common in co-infection of various infections and is peremptory to make an etiologic diagnosis and early treatment.