Background: Rheumatoid arthritis (RA) has increased cardiovascular (CV) events. Standard CV risk factors, including lipid profiles, are not different in RA and it is still unclear how to best evaluate this in RA. Lipoprotein subclasses have been used recently to better assess CV risk and have not been evaluated along with a marker of endothelial function in RA. Methods: Thirty-five seropositive RA and thirty-one control subjects without a history of coronary artery disease, diabetes, or active statin therapy were recruited. Lipoprotein subclass concentration and small arterial elasticity (SAE) - a marker of endothelial function - were measured in both groups and then repeated in the RA group after 12 months. Results: 1. There was no significant difference between the RA and control groups in small arterial elasticity. 2. The RA group had significantly lower total LDL and small LDL particles and increased average HDL size compared to controls. 3. Within the RA group, there was a significant correlation of increased disease activity with reduced small HDL particles. No significant correlations were seen between disease activity with small LDL particles or HDL size. Changes in lipoprotein particles and disease activity did not correlate with changes in SAE. Conclusions: 1. Alterations in LDL subclasses may not account for increased cardiovascular risk in RA. However, reductions in the potentially anti-atherogenic small HDL particles may be a potential factor. 2. Small arterial elasticity did not differentiate RA from controls in assessing cardiovascular risk and was not affected by changes in lipoprotein subclasses.