The relationship between antipsychotic-induced extrapyramidal syndrome (EPS) and the autonomic neurocardiac function was examined in 57 schizophrenic patients treated with atypical antipsychotics. Comprehensive assessments of EPS and heart rate dynamics were performed. There was a significant negative correlation of non-hypokinetic parkinsonism, akathisia, and dyskinesia with several linear and novel non-linear heart rate dynamics measures, suggesting reduced neurocardiac dynamics associated with some forms of EPS. Assessment of heart rate dynamics may be useful for the detection of these adverse effects and may serve as a useful non-invasive method providing a dynamic window into the alterations of complex neuronal activity.