Individual differences in autonomic nervous system reactivity have been studied in relation to physical and mental health outcomes, but rarely among children with chronic disease. The purpose of this study was to examine the associations among autonomic reactivity, clinical severity, family stressors, and mental health symptoms in children with homozygous sickle cell disease. Nineteen children with homozygous sickle cell disease participated in a cross-sectional study involving parent-completed measures, medical record reviews and laboratory-based measures of autonomic nervous system responses to social, cognitive, physical and emotional challenges. Autonomic reactivity was significantly associated with both clinical severity and externalizing behavior symptoms. Children with greater parasympathetic withdrawal during challenges compared to rest had significantly more severe disease (r = -0.45, p < 0.05); greater sympathetic activation during challenges compared to rest was associated with more externalizing behavior symptoms ( r= 0.44, p < 0.05). Children experiencing major family stressors had internalizing behavior symptoms but no difference in autonomic reactivity or clinical severity compared to children experiencing fewer family stressors. Individual differences in autonomic reactivity may offer a new, biologically plausible account for observed variation in painful episodes, other physical complications and behavioral symptoms among children with sickle cell disease.