Schizophrenia is a brain disease whose pathophysiology has escaped detection despite intensive investigation. The failure to delineate the neuroanatomy of schizophrenia is related in part to both the subtle nature of the neuropathological abnormalities and to the failure to address adequately the pathophysiological heterogeneity of schizophrenia. The symptoms of schizophrenia aggregate into relatively independent symptom complexes, which suggests that there may be a distinct neural substrate for each complex. If this is true, then the neuroanatomy of schizophrenia is better addressed as the separate neuroanatomies of symptom complexes. However, the use of symptom complexes to guide future neuroanatomical investigations raises crucial methodological issues, including the differentiation of primary versus secondary symptoms, trait versus state characteristics, and continuous versus categorical variables. Decisive hypothesis testing requires that these issues be addressed in study design.