Abstract The genus Pneumocystis is composed of opportunistic fungi currently considered as specific pulmonary pathogens in humans and other mammals. In pigs, Pneumocystis pneumonia (PcP) could create significant economical losses due to its detrimental effects on growth, food conversion, and carcass/viscera condemnation. This study revealed that Pneumocystis organisms could be detected by Grocott's staining or immunohistochemistry in 36.9% of 564 slaughtered pigs from two geographic regions of Brazil. The prevalence of positive cases was 39.9% and 33.9% in pigs slaughtered in Rio Grande do Sul (RS) and Mato Grosso (MT) states, respectively. Among the positive cases in RS, Pneumocystis organisms were observed in 41.9% of 33 histologically normal lungs, and in 58.0% of lungs presenting with histological lesions. In contrast, the prevalence in MT in normal and abnormal lungs was 36.3% and 63.5%, respectively. Major histopathological findings in lungs of infected animals were bronchointerstitial pneumonia (47.6%), suggestive of enzootic pneumonia, and interstitial pneumonia (37.9%), compatible with PcP. The results of this survey strengthened the interest of detecting fungal pathogens, in addition to other infectious agents, and evaluating their financial impact on Brazilian pig industry. Preventive and/or therapeutic strategies should be developed in order to minimize the incidence of respiratory fungal infections in pigs and associated economic losses.