Radioiodinated apolipoprotein A-I was separated into two pools by gel chromatography on Sephadex G-150 superfine resin or by high performance liquid chromatography using a TSK-2000 column. The first pool, pool 1, was indistinguishable from unlabeled apo-A-I as judged by sedimentation equilibrium, circular dichroic measurements, and radial immunodiffusion. This pool self-associated according to a monomer-dimer-tetramer-octamer scheme and underwent the expected conformation changes with dissociation as reported previously for unlabeled apo-A-I. The radioiodinated material in pool 2 had less secondary structure as compared to the unlabeled material and did not self-associate. Protein in this pool was immunochemically less reactive than unlabeled apo-A-I. Kinetic studies, in vivo, demonstrated that these two pools of radioiodinated apo-A-I are also distinguished metabolically. Discussion centers around possible mechanisms of formation of the incompetent protein in pool 2 and factors that should be taken into consideration when using unfractionated radioiodinated apo-A-I for experimental studies.