123I 15-(p-iodophenyl)-3(R,S)-methylpentadecanoic acid (BMIPP) myocardial scintigraphy and exercise stress thallium (TI)-201 myocardial scintigraphy were performed in 17 patients with hypertrophic cardiomyopathy (HCM) to evaluate the existence of abnormal fatty acid metabolism in the myocardium and the relationship between this abnormality and myocardial ischemia. On the BMIPP scintigraphy, abnormalities were found in 12 of 17 patients (71%). Five patients showing no abnormalities on the BMIPP scintigraphy had well preserved exercise tolerance and had longer exercise duration than the others showing BMIPP scintigraphic abnormalities (P < 0.001). On the evaluation of the segmental abnormalities, TI scintigraphic abnormalities were found in 15 (50%) of 30 segments showing decreased accumulation of BMIPP. On the other hand, BMIPP scintigraphic abnormalities were found in all segments showing decreased accumulation of TI. The sites of decreased accumulation of BMIPP and TI were in good agreement with the sites of wall hypertrophy. Four patients showing BMIPP scintigraphic abnormalities and no T1 scintigraphic abnormalities were in higher New York Heart Association functional classes, had shorter exercise duration (P < 0.05) than the 5 patients showing no abnormalities on either scintigraphy. It is concluded that abnormalities of fatty acid metabolism in the heart are detected at a high rate in patients with HCM, and may be due in part to factors other than myocardial perfusion disturbance.