Methods for reduction of aggregate levels in antibody and other protein preparations through treatment with low concentrations of electropositive organic additives (e.g., ethacridine, chlorhexidine, or polyethylenimine) in combination with ureides (e.g., urea, uric acid, or allantoin) or organic modulators (e.g., nonionic organic polymers, surfactants, organic solvent or ureides). Some aspects of the invention relate to methods for reducing the level of aggregates in conjunction with clarification of cell culture harvest. It further relates to the integration of these capabilities with other purification methods to achieve the desired level of final purification.