Stroke in humans is associated with deficits in sensorimotor and cognitive function. Consequently, many stroke researchers recently have expanded their techniques to assess cognitive and behavioral correlates of histologically-determined stroke damage in animal models. Although the incorporation of functional outcome assessment represents an important step forward in stroke research, reports of middle cerebral artery occlusion (MCAO) induced behavioral deficits often conflict, and a significant correlation between post-stroke histology and behavior has been reported in few stroke studies. Discrepancies in behavioral outcomes among studies may be due to several factors, such as method of MCAO, duration of occlusion, strain, the timing and method of the behavioral testing and the laboratory environment. Furthermore, proper experimental and control groups, necessary to rule out potential confounding factors during cognitive testing, often are not incorporated. The goal of this review is: (1) to provide a description of the techniques most commonly employed to assess functional outcome after (MCAO) in rodents and (2) to identify potential confounding factors that may interfere with a clear interpretation of the behavioral data.