IDL is considered an atherogenic lipoprotein but little progress has been made on methods to subfractionate this density class. Furthermore, previous work suggests that lipoproteins retained by the arterial wall, of which chondoitin sulphate is the major arterial wall proteoglycan, are potentially atherogenic. The aim of this study was to assess the subfractionation of IDL particles using chondroitin sulphate (CS). Forty healthy subjects were recruited from laboratory staff and/or their partners. Fasted plasma samples were obtained and IDL (1.006 g/ml<d<1.030 g/ml) was isolated. Approximately 1mg protein of IDL was allowed to interact with CS. The unbound and bound IDL particles were eluted using a low salt and high salt buffer, respectively. On average 70% of IDL bound to CS ranging from 56 to 92%. Total, unbound and bound IDL particles were analysed for lipid composition and particle size. The unbound IDL particles were larger (32 nm) and triglyceride rich (40% versus 33%, P<0.01), whereas the bound IDL particles were smaller (26-28 nm) and cholesterol rich (21% versus 14%, P<0.01). The unbound particles contain at least double the amount of apo C-II and apo C-III per IDL particle compared with the bound IDL particles. There are specific IDL particles that bind to CS in vitro, these being the cholesterol rich IDL particles. It remains to be determined if these cholesterol rich IDL particles are potentially more atherogenic than the triglyceride rich IDL particles.