Wildlife Research, 2015; 42(2):143-148Context. Toe clipping is a widely used method for permanent marking of small mammals, but its effects are not well known, despite the ethical and scientific implications. Most studies do not find any clear effects, but there is some indication that toe clipping can affect survival in specific cases. Although effects on survival are arguably the most important, more subtle effects are also plausible, yet very few studies have included body condition and none has investigated effects on mobility. Aims. We analysed the effects of toe clipping on free-living Mastomys natalensis, a common, morphologically and behaviourally intermediate small rodent. Methods. Using a 17-year capture–mark–recapture dataset, we compared movement, body weight and survival between newly and previously clipped animals, and tested whether any of these parameters correlated with the number of clipped toes. Key results. No evidence for a correlation between total number of clips and any of the variables was found. Newly clipped animals had a slightly smaller weight change and larger travel distance than did those that were already clipped, and we show that this is most likely due to stress caused by being captured, clipped and handled for the first time rather than to the actual clipping. Conclusions. The combination of trapping, handling and marking has a detectable effect on multimammate mice; however, there is no evidence for a clear effect of toe clipping. Implications. Our study suggests a re-evaluation of ethical guidelines on small-mammal experiments, so as to reach a rational, fact-based decision on which marking method to use.