Dietary manganese affects lipid and lipoprotein metabolism. In the Sprague-Dawley rat, manganese deficiency affects high-density lipoprotein composition and may alter lipoprotein structural stability. This study assessed the effects of manganese on high-density lipoprotein subclass structure, dynamics, and mobility, using fluorescence quenching and fluorescence polarization techniques. Male Sprague-Dawley rats were fed diets deficient or adequate in manganese. High-density lipoprotein 1 (HDL 1 , density 1.05 to 1.077 kilograms/liter) and high-density lipoprotein 2 (HDL 2 , density 1.077 to 1.21 kilograms/liter) were separated by density gradient ultracentrifugation. Iodide quenching of intrinsic (tryptophan) fluorescence showed that there were at least two types of fluorophores in both lipoprotein subclasses. Differences in dynamics and accessibility were noted in HDL 1 (deficient, K s v =16.9 (mol/L) - 1 , f a = 20%; adequate, K s v = 9.8 (mol/L) - 1 , f a = 27%) and in HDL 2 (deficient, K s v = 0.89 (mol/L) - 1 , f a = 100%; adequate, K s v = 4.71 (mol/L) - 1 , f a =36%). Differences in polarized fluorescence emission were seen in HDL 2 but not in HDL 1 (deficient, P = 0.193; adequate, P = 0.213). There were no differences in dynamics, accessibility, or polarized fluorescence in apolipoproteins from either subclass. The data suggest structural changes in HDL 1 and changes in the rotational motion of the proteins in HDL 2 . These changes may affect HDL metabolism in the rat.