The aim of this study was to assess the impact of cardiac autonomic derangement on gender-associated functional outcome of patients with subacute ischemic stroke undergoing a hospital-based rehabilitation program. The study population included 126 consecutive first-ever stroke survivors (mean age 59.7 +/- 11.6 years). Time-domain measures of heart rate variability (HRV) by 24-hour Holter monitoring (HM) were considered in all cases. By the end of the rehabilitation program an unfavorable functional outcome with dependency (Barthel Index score of <75) was found in 27 men (40.3%) and in 31 women (52.5%; p = 0.168). Multivariate analysis demonstrated that high age, low Barthel Index score and low Rankin Scale score on admission were independent predictors of an unfavorable functional outcome in both men and women. The standard deviation of normal-to-normal RR intervals on HM was an independent predictor of rehabilitation outcome only in men (OR 15.29, 95% CI 2.47-46.58, p = 0.001). The presence of insular damage on neuroimaging studies was independently associated with an unfavorable functional outcome only in female (OR 18.89, 95% CI 2.34-71.4, p = 0.006). HRV does not predict functional outcome after rehabilitation in women. Instead, insular damage appears to have a role in determining the final results of rehabilitation in women but not in men.