The complexity of the T wave assessed by principal component analysis (PCA) has been proposed to reflect abnormal repolarization, which may be arrhythmogenic. To determine whether PCA can differentiate patients with hypertrophic cardiomyopathy (HCM) from normal subjects and whether PCA is of prognostic importance in HCM, 112 patients with HCM (41 +/- 14 years, 64 males) and 72 healthy subjects (39 +/- 9 years, 41 males) were studied. Patients with sinus node dysfunction, AV conduction block, flat T waves, QRS > 140 ms, and those < 15 years were excluded from this study. Standard 12-lead ECGs were recorded digitally using the MAC-VU system (Marquette Medical Systems). PCA parameters were computed using the QT Guard software package by Marquette. PCA ratio was significantly greater in HCM patients than in normal controls (23.9% +/- 12.4% vs 16.1% +/- 7.6%, P < 0.0001) and was correlated with QT-end dispersion (r = 0.24, P = 0.01) and QT peak (Q point to T peak) dispersion (r = 0.35, P < 0.0001). HCM patients with syncope (n = 23) had increased PCA ratios compared with those without syncope (29.1% +/- 11.5% vs 22.5% +/- 12.3%, P = 0.01). PCA ratio was similar in patients with and without nonsustained ventricular tachycardia on Holter (25.9% +/- 11.4% vs 22.7% +/- 12.1%, P = 0.2), as well as in patients treated with amiodarone or sotalol versus those not on therapy. In conclusion, assessment of the complexity of the T wave by PCA differentiates HCM patients from normal subjects. PCA ratio correlated with QT dispersion and an increased PCA ratio was associated with a history of syncope in HCM.