This study extends a previous study of the factor structure of the neurologic examination in unmedicated schizophrenia, utilizing cluster analysis and adding a medicated condition. We administered a modified version of the Neurologic Evaluation Scale (NES) on two occasions to 80 patients with schizophrenia or schizoaffective disorder, once while on antipsychotic medications and once while off medication. Data were distilled by combining right- and left-side scores, and by excluding rarely abnormal and unreliable items from the analysis. Principal components analysis yielded an intuitive four-factor solution in the unmedicated condition, but an inscrutable five-factor solution during medication. Cluster analysis revealed three groups: normal, cognitively impaired, and diffusely impaired. These results were also less interpretable with data from the medicated condition. Neurologic performance was better in the medicated than in the unmedicated condition. As is the case with other domains of symptoms and performance in schizophrenia, relationships among neurologic exam variables are altered by the presence of antipsychotic medication.