To investigate the associations of high-density lipoprotein (HDL) subfractions and apolipoprotein A-I (apo A-I) with fat in the pancreas. A total of 170 individuals were studied. All participants underwent magnetic resonance imaging on a single 3.0-Tesla scanner to determine the presence/absence of fatty pancreas. HDL subfractions were measured using a commercially available lipoprotein subfractions testing system and classed as large, intermediate and small HDL. Both unadjusted and adjusted (accounting for demographics, anthropometrics, insulin resistance and other covariates) logistic regression models were built. Individuals with fatty pancreas had significantly lower circulating levels of the large HDL class and apo A-I. Every unit decrease in the large HDL class was associated with a 93% increase in the likelihood of fatty pancreas in the most adjusted model (P < .001). Every unit decrease in apo A-I was associated with a 45% increase in the likelihood of fatty pancreas in the most adjusted model (P = .012). The intermediate and small HDL classes were not significantly associated with fatty pancreas. Fat in the pancreas is inversely associated with the circulating levels of large HDL particles and apo A-I. Purposely designed studies are warranted to investigate the potential of fatty pancreas as an indicator of the risk of cardiovascular diseases.