T wave alternans that is visually apparent on the ECG is a known risk factor for sudden death in idiopathic long QT syndrome (LQTS). To determine if occult and visually undetectable forms of T wave alternans are also present in LQTS, we measured T wave alternans from a 16-year-old girl with LQTS during exercise using spectral analysis methods and a recording system designed to minimize exercise-related noise. While there was no alternans at rest, statistically significant, yet visually inapparent T wave alternans were measured both during exercise and recovery. Using identical recording techniques, no significant T wave alternans was detected from the subject's mother, who had a prolonged QT interval but was not experiencing arrhythmias, nor from five healthy volunteers with normal QT intervals. This report suggests that electrocardiographically occult, yet prognostically important forms of T wave alternans may be present in patients with LQTS.