LDL particle size can be measured by gradient gel electrophoresis (GGE) and NMR. The agreement between the two methods has not been extensively evaluated. Therefore, we measured LDL size by NMR and GGE in 324 individuals (152 with type 1 diabetes and 172 controls). The Spearman correlation between both methods was 0.39 [95% confidence interval (CI) = 0.29, 0.48]. The average difference was 5.38 nm (NMR being smaller), but it increased with increasing LDL size. Less than 50% of people classified as pattern B on GGE were classified as pattern B on NMR (kappa = 0.31; 95% CI = 0.17, 0.45). Agreement was lower for diabetic subjects compared with controls, for women compared with men, and for subjects with triglycerides less than 1.30 mmol/l compared with subjects with triglycerides greater than 1.30 mmol/l. External validation showed that cholesteryl ester transfer rate was related to LDL size on GGE in all subgroups and to LDL size on NMR only in men and nondiabetic subjects. Our findings show that agreement between NMR- and GGE-based LDL size is far from perfect and is not consistent across subgroups of patients. In particular, the two methods should not be assumed to be interchangeable in women and diabetic subjects. Whether NMR or GGE predicts cardiovascular disease risk better has not yet been evaluated.