The cause of abnormal Q waves in hypertrophic cardiomyopathy remains unclear. Myocardial wall thickness was assessed by two-dimensional echocardiography at 8 left ventricular and 10 right ventricular sites in 67 patients (mean age 40 years) with hypertrophic cardiomyopathy and the findings were analyzed in relation to the presence of abnormal Q waves on the 12 lead rest electrocardiogram (ECG). Nineteen (28%) of the 67 patients had abnormal Q waves. Right ventricular hypertrophy was significantly more common in patients without abnormal Q waves (25 [52%] of 48 versus 2 [11%] of 19, p less than 0.001). With univariate analysis, there were six measurements that were significantly associated with abnormal Q waves: an increase in upper anterior septal thickness (p less than 0.005) and maximal left ventricular wall thickness (p less than 0.02), a decrease in mean and maximal right ventricular wall thickness (both p less than 0.005) and an increase in the ratio of both upper anterior septal to mean right ventricular wall thickness (p less than 0.005) and upper anterior septal to upper posterior wall thickness (p less than 0.005). With multivariate analysis, only the ratios of upper anterior septal to mean right ventricular wall thickness (p less than 0.005) and to upper posterior wall thickness (p less than 0.05) were significantly related to the presence of abnormal Q waves and predicted Q wave location with a sensitivity, specificity and predictive accuracy of 90%, 88% and 89%, respectively. In hypertrophic cardiomyopathy, the presence of abnormal Q waves on the 12 lead ECG is primarily a function of the relation of right ventricular wall thickness and upper anterior septal thickness.