In order to achieve higher efficiency of training and thus better athletic performance, new research and diagnostic methods are constantly being developed, particularly those that are non-invasive. One such a method is thermography, suitable for quantitative and therefore objective evaluation of variables, such as changes in the temperature of the skin covering working muscles. The aim of this study was to use a thermal imaging infrared camera to evaluate temperature changes of symmetric body surfaces over symmetrically working muscles of male scullers after exercising on a two-oared rowing ergometer and compare these to asymmetrically working muscles of handball players after an endurance training session containing elements of an actual game. In the scullers, the mean temperature of body surfaces was always lower post than pre exercise, with no significant differences in an average temperature drop between the opposite sides, indicating that the work of the muscles involved in the physical exertion on the rowing ergometer was symmetrical. In contrast, in the handball players, skin temperatures in symmetric areas over the asymmetrically working muscles showed statistically significant differences between sides, which was associated with the functional asymmetry of training. This study indicates that thermal imaging may be useful for coaches in the evaluation of technical preparations in sports in which equal involvement of symmetric muscles is a condition of success, e.g. in scullers.