Nonalcoholic fatty liver disease (NAFLD) is an emerging, highly prevalent, cardiovascular risk factor, and lipoprotein proatherogenic disturbances likely explain a large part of this risk. However, information regarding associations between detailed nuclear magnetic resonance (NMR) lipoprotein changes and noninvasive NAFLD scores is lacking. The objective of the study was to investigate the NMR-assessed atherogenic lipoprotein profile according to noninvasive NAFLD status. Lipoprotein profiles by NMR spectroscopy and NAFLD status by fatty liver index (FLI) and Gholam's models. We assessed 173 participants (55% males), mean age 60.8±7.8years, 87% overweight/obese, 53% with diabetes. An FLI <30, 30 to 60, and >60 was found in 32, 50, and 91 participants, respectively. Individuals with FLI >60 had lower high-density lipoprotein (HDL)-cholesterol (P<.001), higher triglyceride (P<.001), and similar non-HDL-cholesterol (P=.912) concentrations. In NMR analysis, FLI was related with very-low-density lipoprotein (VLDL) and HDL parameters in a dose-dependent manner. VLDL particle number (P<.001) and VLDL size (39.1±0.99, 39.7±0.96, 40.8±1.19nm, P<.001) increased with increased FLI (<30, 30-60, and >60, respectively). Conversely, although total HDL particle number did not differ by FLI (P=.377), larger HDL particles (P<.001), amount of cholesterol within HDL particles (P<.001), and HDL size (median [p25-p75]: 8.23 [8.08-8.41], 8.12 [8.03-8.29], 8.04 [7.93-8.16]nm, P<.001) decreased as FLI increased. FLI >60 (vs <60) was associated with a higher proportion of small LDL particles (P=.010) and lower LDL size (19.85±0.34 vs 19.98±0.25nm; P=.005). Similar findings were found for Gholam's model. Simple and noninvasive NAFLD scores are useful to detect many of the proatherogenic changes (especially in VLDL and HDL), beyond conventional lipids parameters that are common in individuals with this high-risk condition.