The objective of this study was to investigate cholesterol metabolism and its association with glucose metabolism and genetic regulation in metabolic syndrome. Overall, 74 subjects with clinically defined metabolic syndrome and sex and age-matched controls (n=74) were recruited. Cholesterol metabolism was assayed with serum non-cholesterol sterols, surrogate markers of synthesis, and fractional absorption of cholesterol and was related to variables of glucose and insulin action and to the common polymorphisms of the ABCG5 and ABCG8 genes. Serum squalene and non-cholesterol sterols were analyzed with gas-liquid chromatography (GLC) and presented as ratios to cholesterol. Also, synthesis marker/absorption marker ratios were calculated. The subjects with metabolic syndrome had higher cholesterol synthesis marker ratios, including squalene, and lower absorption marker ratios than controls. When adjusted with body mass index (BMI) and waist circumference, differences in some of the absorption markers (plant sterols), but not in the synthesis markers, disappeared. Plasma glucose, serum triglycerides, and homeostasis model assessment (HOMA) index were positively associated with cholesterol synthesis/absorption marker ratios (r=0.264 to 0.353, P<0.05 for all). In multivariate analysis, the serum squalene ratio was the best variable of those of cholesterol metabolism explaining the presence of metabolic syndrome. The polymorphisms of ABCG5 and ABCG8 genes did not differ between the cases and controls. In conclusion, cholesterol synthesis prevails over absorption in metabolic syndrome. The high serum squalene ratio turned out to be associated with the prevalence of metabolic syndrome. The perturbations of cholesterol metabolism seem to be related to abdominal obesity, and weight reduction might normalize cholesterol metabolism.