Experimental stroke treatment by mesenchymal stem cell (MSC) populations is an attractive paradigm in stroke research. There are many studies describing improved functional outcomes after MSC delivery in stroke, but the mechanisms through which the transferred cells exert these effects are less well understood. Moreover, commonly applied functional tests may not be suitable for discriminating real functional recovery from compensation, which is a frequently encountered phenomenon in rodents. This commentary highlights some of the potential risks for the translational process associated with these tests and proposes some alternative test arrays which may achieve more specific functional phenotyping.