Clarithromycin is a promising drug for the treatment of Mycobacterium kansasii infection. We report a patient with AIDS and severe M. kansasii infection who had previously received a short course of clarithromycin for sinusitis. He had clinical failure of treatment using clarithromycin plus ethambutol, and the initial isolate was found to be highly resistant to clarithromycin. Nucleotide sequencing of the 23S rRNA gene of this isolate demonstrated a single base mutation at position 2058, the same as that found in clarithromycin-resistant Mycobacterium avium.