Background and aims Patients with inflammatory bowel disease (IBD) are at increased risk for coronary artery disease (CAD), even after adjusting for traditional risk factors for atherosclerosis. While inflammation is widely regarded as the pathophysiologic link between IBD and CAD, the exact mechanisms are largely unknown. This study was conducted to investigate the association of lipid parameters and indices with coronary flow reserve and markers of inflammation in IBD patients. Methods A total of 73 patients with IBD and 26 healthy controls were enrolled. Patients in the IBD arm were either in remission or had mild disease activity. Lipid parameters, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) were analyzed using standard laboratory techniques. Coronary flow reserve (CFR) was measured using two-dimensional echocardiography. Results Both CRP and ESR were higher and CFR was significantly lower in IBD patients, but there were no differences in terms of lipid parameters or indices; however, patients with IBD and a CFR <2.0 had significantly higher triglyceride (TG) level (155.0 (80.0)& x202f;mg/dl vs. 108.0 (68.0)& x202f;mg/dl, p & x202f;< 0.001) and there was a strong trend towards lower high-density lipoprotein (HDL) cholesterol (40.0 (8.5)& x202f;mg/dl vs. 45.0 (10.0)& x202f;mg/dl, p & x202f;= 0.05) level in the latter group when compared to patients with a CFR >= 2.0. The atherogenic index of plasma (AIP), measured as log(TG/HDL-C) had the best predictive value for CFR in IBD group and was an independent predictor of CFR after multivariate adjustment for confounders (unstandardized coefficient: -0.75, 95% CI: (-1.13)-(-0.37)), beta & x202f;= -0.41, p & x202f;= <0.001). Conclusion The atherogenic index of plasma is a marker for reduced CFR in IBD patients and could be useful to screen those at risk for early atherogenesis and CAD.