This study was focused on the thermal mapping of skin over the selected muscle zones in two groups of elite athletes fully engaged in completely other sports performing about an hour running effort at individual AT intensity. Two groups of elite male athletes, a group of cross-country skiers (CS; N = 6) and a group of elite endurance swimmers (SW; N = 4), were investigated. Thermal images of sportsmen’ body at front and from the rear were recorded before and about 1–2 min after exercise test using camera Flir Systems E60. Functional (heart rate, oxygen uptake, workload) as well as biochemical markers (activities of creatine kinase and lactate dehydrogenase, concentration of lactate and haemoglobin) were also assessed. The marked differentiation in skin temperature distribution in cross-country skiers and endurance swimmers subjected to the same endurance exercise on treadmill was observed. There was significant decrease in temperature in upper body temperature in CS group, while SW group revealed a significant increase in temperature of the lower limbs. The calculated total body skin temperature was also influenced by practicing training of elite athletes. Some significant correlations of physiological, biochemical and morphological parameters (% fat) with average temperature after exercise test were found for different muscle zones in swimmers and cross-country skiers. Statistical analysis showed that workload had the most impact on skin temperature changes, especially in swimmers. The results provide additional information on the muscle work in the different sport disciplines and may be helpful in efficiency evaluation of elite athletes.