Central nervous system comorbidities have been identified in patients with epilepsy. Several of these comorbidities have been correlated with poor surgery outcomes in patient cohorts. The authors sought to determine if prevalence of comorbidities in pediatric epilepsy surgery patients and their families correlate with long-term seizure outcome in a cross-sectional analysis. Three-generation pedigrees were elicited to compare family history of epilepsy, ADHD, anxiety, autism, bipolar disorder, cognitive disability, depression, migraine, and motor disability to surgery outcomes in 52 patients. Proportions of affected patients and relatives were compared to general population comorbidity rates and the patients’ most recent seizure outcome classification. Patients and families had significantly higher rates of comorbidities than the general population. Poorer long-term seizure outcomes following resective surgery were associated with autism or cognitive disability in patients. Together these data support evidence for a common pathophysiological mechanism between epilepsy and central nervous system comorbidities.