Eyes with pseudoexfoliation syndrome have a greater risk of intraoperative and postoperative complications. Clinical and histopathological studies indicate that heparin-surface-modified intraocular lenses (HSM IOLs) can reduce postoperative anterior segment inflammation. Our study evaluated the blood-aqueous barrier permeability in eyes with pseudoexfoliation syndrome and implanted with an HSM IOL. We examined two groups of 20 patients, one comprising patients with pseudoexfoliation syndrome and one a sex- and age-matched control group with senile cataracts. Each group was divided into two subgroups of ten patients each. In one subgroup, an HSM IOL was implanted; in the other, a conventional poly(methyl methacrylate) IOL. We performed a complete ophthalmologic examination and iris angiography preoperatively and at 30, 90, and 180 days after surgery. Fluorophotometry was performed at the 90-day and 180-day postoperative examinations. The patients with pseudoexfoliation syndrome had a higher blood-aqueous barrier permeability than did the control group. Permeability decreased significantly three and six months after surgery, especially in the HSM IOL group.