Intraocular lens (IOL) insertion is now the standard method of aphakic correction in this country. Previous studies have shown that an IOL can activate the alternative complement system of normal human serum in vitro, thereby generating peptides capable of stimulating inflammation that can result in visual morbidity in pseudophakic eyes. The objective of the present study was to determine if human aqueous humor (AH) levels of total protein, total C3, and C3a cleavage products (activated C3) are influenced by an IOL in pseudophakic eyes as compared with phakic and aphakic eyes. AH from five diagnostic categories was examined: cataract, posterior capsulotomy-IOL, Fuchs' endothelial dystrophy with corneal edema, aphakic bullous keratopathy, and pseudophakic bullous keratopathy. The results of this study do not support the hypothesis that IOLs affect AH protein and complement levels. Statistically, there was no significant difference in AH protein levels when pseudophakic eyes were compared with phakic and aphakic eyes. No significant difference in C3a levels was demonstrated between pseudophakic and phakic eyes, whereas aphakic eyes had significant higher levels than those with pseudophakia. There were significantly greater levels of protein, C3, and C3a in eyes with edematous corneas versus those with clear corneas. Although these studies are difficult to interpret, AH levels of these substances appear to be more related to dysfunctional corneal endothelium and corneal edema than to the presence of an IOL.