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Patients referred to rehabilitation centers often suffer from associated comorbidity, which might negatively influence the effective outcome of the treatment program. The study was aimed at evaluating the impact of comorbidity on functional independence and gain after stroke. Ninety-three patients admitted to rehabilitation were enrolled. The disability was evaluated, both at time of admission and at discharge. The functional independence measure (FIM) was used. Comorbidity was evaluated by means of the Cumulative Illness Rating Scale (CIRS), that generates two indexes, the cumulative index (CI) and the severity index (SI). A logistic model could discriminate patients who were regularly discharged from the others (dead or transferred to acute care) pooled together (P ≤ 0.02). The CI and SI were significantly correlated with FIM at admission. The r-values were −0.24 (P ≤ 0.02) and −0.32 (P < 0.002). Recovery was not even influenced in the most severe patients. In conclusion, the CIRS appears to be a sensitive tool for the evaluation of comorbidity in stroke patients. The comorbidity is correlated to dependence in stroke patients but does not affect functional gain. However, comorbidity is of actual interest in view of new payment systems in rehabilitation, because it is included among the variables leading to costs.