Apathy and hypersomnia occur after stroke and, by definition, reduce participation in rehabilitation, but their effect on outcome from acute rehabilitation is not known. We performed a retrospective review of 213 patients admitted to a stroke-specialized acute rehabilitation unit in the United States. All patients had ischemic or hemorrhagic stroke, and no dementia or dependence on others pre-stroke. We diagnosed apathy and hypersomnia using standardized documentation by treating therapists. We used multiple regression analysis to control for overall impairment (combination of strength, cognitive and sensory measures), age, time since stroke, and stroke type (ischemic or hemorrhagic). Forty-four (21 %) of the patients had persistent apathy, and 12 (5.6 %) had persistent hypersomnia. Both groups were more impaired in cognition, sustained attention, and more likely to be treated for depression. Patients with apathy were 2.4 times more likely to go to a nursing home, and had discharge FIM scores 12 points below the mean. Patients with hypersomnia were ten times more likely to go to a nursing home, and had discharge FIM scores 16 points below the mean. These findings indicate that studies to prospectively define these clinical factors and potential confounds using standardized tools are indicated, and if confirmed, justify studies to identify these patients early and develop targeted interventions.