In a review of more than 2000 MR images of the brain we identified 35 patients with absence of the septum pellucidum. These patients were divided into seven basic groups as follows: septooptic dysplasia; schizencephaly; holoprosencephaly; agenesis of the corpus callosum; chronic, severe hydrocephalus; basilar encephaloceles; and porencephaly/hydranencephaly. Absence of the septum pellucidum was never seen as an isolated finding. By using data gathered from the review of the MR scans of patients in this study, we devised a diagnostic algorithm to aid in the classification of these patients. Absence of the septum pellucidum can provide a valuable clue to the diagnosis of malformations of the brain.