Oral lesions are rarely reported in paucibacillary forms of leprosy. We report here a case with an erythematous hyposensitive lesion in the palate and no skin lesions. In addition to routine tests, biopsies of the lesion in the palate and of clinically normal surrounding areas were performed and subjected to real-time PCR for detection of Mycobacterium leprae DNA. The biopsy of the oral lesion was positive for bacilli DNA, followed by positive serum anti-PGL-1 and Mitsuda test, but with negative histopathology. The patient was diagnosed with a borderline tuberculoid form. After multidrug therapy the lesion had significantly regressed and the bacilli DNA detection in the former lesion was negative. The bacilli DNA detection in an oral lesion by real-time PCR not only improved leprosy diagnosis, but also helped in the classification of clinical form, and in the establishment of the appropriate therapeutic regime.