Aspergillosis is a fungal disease caused by the inhalation of fungal spores of the genus Aspergillus spp. This fungus mainly affects the lungs but can spread and infect the maxillofacial region through the bloodstream. The disease has nonspecific clinical manifestations, which hinders early diagnosis. Even though the Polymerase Chain Reaction (PCR) technique holds promising potential to aid in diagnosing aspergillosis, anatomopathological analysis services have not yet routinely adopted the method. Therefore, the present study aims to evaluate the applicability and standardize the techniques of preparation of biological samples and PCR for the detection of the species Aspergillus niger, Aspergillus fumigatus and Aspergillus flavus. Six samples of formalin-fixed, paraffin-embedded tissue (FFPE), with histopathological diagnosis suggestive of aspergillosis, were investigated by PCR. Five of the six samples evaluated were positive for the fungus Aspergillus spp, 2/5 of which were co-infected by A. fumigatus and A. flavus species, and the others were positive for A. flavus species. The findings of this study suggest that PCR may be an auxiliary method in diagnosing aspergillosis. However, the expansion of the sample size and the evaluation of PCR in comparison with other diagnostic tests for aspergillosis is essential to determine the accuracy of the method.