Preparation of apolipoprotein B (Apo B)-deoxycholate (DOC) complexes by gel filtration chromatography in the presence of 20 mM DOC, pH 8.5, gave two populations of particles with 5% (peak I) and 13% (peak II) lipid remaining bound. These complexes were initially shown to be very large and elongated, with partition radii of approx. 131 +/- 0.5 A, weight average molecular weights of approx. 164 000 +/- 1 000, and an intrinsic viscosity of 80.19 +/- 2.21 ml/g. Additionally, they appeared very similar to native low-density lipoprotein on sodium dodecyl sulfate-polyacrylamide gels, giving one major band. Incubation of these samples for 10 days under nitrogen at 4 degrees C in the presence of antibiotics and protease inhibitor resulted in dissociation to many smaller subunits. Results of scanning molecular sieve chromatography and analytical ultracentrifugation showed that dissociation of these complexes was relatively slow and indicated the presence of at least two classes of components in fresh samples: one a very elongated complex with a radius directly correlated to the DOC/Apo B ratio and inversely correlated to sample aging; and another of much smaller radius which was independent of DOC/Apo B ratio but directly correlated to sample aging; indicating that these dissociated subunits interact with each other to an appreciable extent. Furthermore, these complexes were found to undergo a preferential hydration upon interaction with DOC, which may contribute to large changes in their effective specific volumes, as well as to dissociation of subunits.