Prolonged exercise is known to increase steady-state serum high-density lipoprotein cholesterol (HDL-cholesterol) and apolipoprotein AI(apo AI) concentrations. We investigated the effect of adaptation to endurance exercise on the association of the genetic polymorphism in the apo AI gene with these biochemical parameters. 108 male subjects were randomly selected from a group of elite athletes, and 65 male samples used as sedentary control group from Korean general population. The genetic polymorphism in the apo AI gene locus was detected by polymerase chain reaction(PCR) and DNA digestion with Msp I restriction endonuclease. The genotype frequency for the Msp I RFLP was significantly different between the elite athletes and sedentary controls(P<0.05). There were, however, no significant associations between the Msp I RFLP of the apo AI gene and the biochemical parameters in elite athletic group. Therefore, our findings indicate that the Msp I RFLP of the apo AI gene was not associated with the serum apo AI and HDL-cholesterol concentrations in Korean male elite athletes.