This study aims to evaluate and predict outcome as part of routine quality assessment of an inpatient stroke rehabilitation programme. By relating functional outcome to patient characteristics, including variables from the quality of life domain, we aim to find a set of variables that can be useful for prognosis, stratification and programme improvement. Data were collected, before and after rehabilitation, from a prospective quality registration database. Included were 250 patients in inpatient stroke rehabilitation after sustaining a first or recurrent ischemic or haemorrhagic stroke. Functional status was measured with the Barthel Index and the Academic Medical Centre Linear Disability Score. Health-related quality of life (HrQoL) was measured with the COOP/WONCA and the Nottingham Health Profile. Significant improvements were found on all outcome measures. A lower functional admission score, older age, more severe stroke, more pain and more negative emotional reactions on admission were found to be independent predictors of a lower outcome score, explaining 39.5% of its variance. Subjective (HrQoL) factors such as negative emotion and pain have an adverse effect on outcome of stroke rehabilitation, in addition to stroke severity, age and functional status at admission. These factors need to be taken into account in screening, clinical decision making and treatment design.