Abstract Background We herein present a case in which a Toxoplasma cyst was found in a transbronchial biopsy specimen from an immunocompetent patient with negative serology for the parasite. Case presentation An 18-year-old Brazilian man presented with a 1-week history of dyspnea and fever and was diagnosed with right lower lobe pneumonia. He began inpatient treatment with intravenous antibiotics. During treatment, a bronchoscopy with bronchoalveolar lavage and transbronchial biopsy was performed. Anatomopathological examination of the transbronchial biopsy showed a small fragment of lung parenchyma with discrete septal thickening and a rounded structure, suggestive of a pseudocyst containing Toxoplasma gondii bradyzoites. However, serological tests were negative for immunoglobulin G and immunoglobulin M. Conclusions Bronchoscopy is a minimally invasive, effective diagnostic and therapeutic method. Despite the fact that the Toxoplasma pseudocyst in the present case was not the cause of the patient’s comorbidities, bronchoscopy with transbronchial biopsy allowed for an incidental diagnosis of a Toxoplasma pseudocyst with minimal invasiveness.