Ameliorating stroke induced neurological deficits is one of the most important goals of stroke therapy. In order to improve stroke outcome, novel treatment approaches as well as animal stroke models predictive for the clinical setting are of urgent need. One of the main obstacles in experimental stroke research is measuring long-term outcome, in particular in mouse models of stroke. On the other hand, assessing functional deficits in animal models of stroke is critical to improve the prediction of preclinical findings. Automated gait analysis provides a sensitive tool to examine locomotion and limb coordination in small rodents. Comparing mice before and 10 days after experimental stroke (60min MCAo) we observed a significant decrease in maximum contact area, stride length and swing speed in the hind limbs, especially the contralateral one. Mice showed a disturbed interlimb coordination represented by changes in regularity index and phase dispersion. To assess whether gait analysis is applicable to assess improvements by neuroprotective compounds, we applied a model calculation and approached common statistical problems. In conclusion, gait analysis is a promising tool to assess mid- to long-term outcome in experimental stroke research.