It seems likely that the neuropeptide Y (NPY)-leptin axis is involved in the regulation of energy expenditure in man. The purpose of this study was to observe the effect of a model of intense prolonged exercise-mediated energy expenditure (25 km swim race in 6.9-10.5 hours) on leptin and NPY concentrations in male long-distance swimmers. Sixteen long-distance swimmers (mean age 25, range 18-45 years) who took part in a 25 km sea swimming competition (Toroneos golf, Chalkidiki, Greece) participated in the study. Mean competition time was 8.5 hours (range 6.5-10.5). The participants were allowed food and beverage intake ad libitum before and throughout the 25 km race. Venous blood samples were taken prior and immediately after the race for the measurement of serum leptin and plasma NPY. Non-esterified free fatty acids (NEFFA) and glycerol levels were determined as indicators of adipose tissue lipids mobilization. Results showed that leptin levels after marathon swimming were significantly reduced (p<0.001) in all athletes. There was a statistically significant negative correlation (r=-0.812, p<0.01) between the values of leptin and glycerol just after the termination of swimming. Blood serum glycerol and free fatty acid levels were significantly increased (p<0.001) in all swimmers. Plasma NPY levels were also increased (p<0.01) in 81.2% of the swimmers. Linear regression analysis revealed a significant negative correlation between the values of leptin and NPY (r=-0.789, p<0.01). In conclusion, these data support our initial hypothesis that appropriate changes in leptin and NPY take place during marathon swimming to compensate for the negative energy balance produced due to this prolonged effort. This indicates the NPY-leptin axis involvement in the regulation of energy expenditure in man.