BACKGROUND: Apolipoprotein (apo) M may exert anti-atherogenic properties in experimental studies. Its hepatic gene expression may be linked to glucose and lipid metabolism. Plasma apoM is decreased in obese mouse models. We hypothesized that plasma apoM is lower in metabolic syndrome (MetS) subjects, and determined whether intima media thickness (IMT) is associated with apoM. METHODS: In 19 non-diabetic subjects with and 60 non-diabetic subjects without MetS (NCEP, ATP III criteria), the relationships of plasma apoM with obesity, glucose, insulin, lipids and adipokines, as well as with IMT were determined. RESULTS: Plasma apoM was on average 15% lower in subjects with MetS compared to subjects without MetS (p=0.036). ApoM correlated inversely with body mass index and waist circumference (p<0.001), and positively with total cholesterol, LDL cholesterol and apoA-I (p<0.05). ApoM was not significantly correlated with glucose, insulin, leptin, adiponectin or resistin (p>0.20). Age- and sex adjusted IMT was lower in subjects with MetS (p<0.05), but was unrelated to apoM (p=0.68). In a multiple linear regression model that included the presence of both MetS and apoM, IMT was only related to MetS (p=0.05). CONCLUSIONS: Plasma apoM is reduced in MetS. In this study, apoM did not predict subclinical atherosclerosis.