This study evaluated physical, chemical and morphological changes in lungs of mice infected with Paracoccidioides brasiliensis. The animals were inoculated with 0.1 mL of fungal suspension of the P. brasiliensis 18 isolate and were euthanized 1, 2, 4 and 8 weeks after inoculation. The upper left lobe of the lung was isolated, fixed and processed for paraffin embedding. The sections were stained with H&E for histopathological study, with Gomori-Grocott to locate and identify the fungus, and with TUNEL immunostaining to detect the occurrence of programmed cell death. The lower and middle right lobes were analyzed by Fourier Transform Infrared Photoacoustic Spectrocopy (FTIR-PAS) to investigate physical and chemical features of the infected lungs. The results showed that lungs infected by P. brasiliensis underwent structural changes that varied according to the time period analyzed, and that changes in the absorption bands of different chemical groups resulted from these morphological changes. The results suggest that the combination of FTIR-PAS spectroscopy with morphological evaluation is an effective procedure for the study of paracoccidioidomycosis, one of the most important systemic mycoses that can damage the lung architecture and consequently impair the respiratory function.