BACKGROUND: Low high density lipoprotein-cholesterol (HDL-C) is one of the major risk factors for coronary heart disease. Using data from the Korean National Health and Nutrition Examination Survey (KNHANES), we assessed trend of the prevalence of low HDL-C and the factors which are associated with low HDL-C in Korean men. METHODS: We analyzed three serial KNHANES data which were conducted in year 1998, 2001, and 2005. Among all survey participants, we included men aged 30-79 years with laboratory data. Low HDL-C was defined by serum HDL-C < 40 mg/dL. We used multiple logistic regression analysis to assess the association between low HDL-C and related factors. We investigated trend of the prevalence of low HDL-C and associated factors among Korean men. RESULTS: The prevalence of low HDL-C in Korean men was increasing from 26.3% (1998) to 38.8% (2001) and 45.9% (2005). Low HDL-C was associated with non-alcohol drinker, current smoking, sedentary physical activity, obesity and hypertriglyceridemia. The prevalence of current smoking decreased linearly. The prevalence of sedentary physical activity and hypertriglyceridemia increased from year 1998 to year 2001, but decreased from year 2001 to year 2005. However, the prevalence of non-alcohol drinker and obesity increased continuously. The patterns of the increasing prevalence of low HDL-C were compatible to the increasing prevalence of obesity according to age in Korean men. CONCLUSION: From year 1998 to year 2005, the prevalence of low HDL-C in Korean men has increased. Obesity and non-alcohol drinking might be contributing factors of increasing prevalence of low HDL-C in Korean men. Management of obesity is needed to prevent increasing the prevalence of low HDL-C among Korean men.