A prospective study was performed in 200 paracoccidioidomycosis (PCM) patients, 51 presenting the acute/subacute form (AF) and 149 the chronic form (CF), submitted to the evaluation of the hepatobiliary system at admission and during the follow-up treatment with cotrimoxazole (CMX) or itraconazole (ITC). This study aimed to better evaluate the involvement of the hepatobiliary system in PCM and the effect of these antifungal compounds on this system. Serum levels of direct bilirubin (DB), total bilirubin (TB), aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), and gamma-glutamyl transferase (GGT) were evaluated. At admission, all the variables showed changes with elevated values ranging from 6.2% for TB to 32.6% for GGT. After treatment, the incidence of elevated serum levels ranged from 3.6% for DB to 27.5% for ALT. The course of the alterations during the treatment showed regression to normal values in CMX-treated patients and persistence in ITC-treated patients but without the need to discontinue the therapy. Our findings contribute to the knowledge of the hepatobiliary involvement by Paracoccidioides sp. and to a safe follow-up of PCM patients under treatment.