The presence of numerous abnormally arranged cardiac muscle cells in the ventricular septum has been considered a characteristic anatomic feature of patients with hypertrophic cardiomyopathy. To determine the specificity of this histologic marker for patients with hypertrophic cardiomyopathy, we used a quantitative method to determine the area of myocardium occupied by disorganized cells. In hypertrophic cardiomyopathy, septal disorganization was present in 94% of the 54 patients studied at necropsy. Furthermore, disorganization was extensive in most of these patients, involving 5% or more of the transverse plane tissue section in 89% of the patients and 25% or more of the section in 56% of the patients. Septal disorganization was best identified in tissue sections cut perpendicular to the long axis of the left ventricle. Septal disorganization was present in only 26% of the 144 control patients with other heart diseases or normal hearts. Most important, when present in these patients, disorganization was usually limited in extent. In only 7% of the controls studied did abnormally arranged cells occupy 5% or more of the tissue section. The average area of septum disorganized was 31 ± 3% (mean i SEM) in patients with hypertrophic cardiomyopathy and only 1.5 ± 0.6% in the controls (p>0.001). Hence, while the presence of ventricular septal disorganization is not pathognomonic of hypertrophic cardiomyopathy, widespread distribution of this abnormality is a very sensitive and specific histologic marker for this disease.