Anodic stripping voltammetric (ASV) procedure, using mercury film electrode, was optimized and applied to determine the concentrations of zinc, cadmium, and copper in the aqueous humor. Concentration levels as low as 1 ppb of the test metals was possible to be detected using short electrolysis times (120 s) and microquantities of aqueous humor (up to 35 μL). As a first application of the voltammetric analysis of trace metals in the aqueous humor, the role of the three selected trace elements in the pseudoexfoliation (PEX) syndrome was examined. Samples from aqueous humor were collected during cataract extraction from patients with and without PEX. The zinc and copper concentration levels in the aqueous humor did not show statistically significant difference in the study and control group. Cadmium was detected in a small number of samples, without however statistical differences between the two groups. ASV proved to be a highly precise and sensitive tool for the quantification of heavy metal ions in aqueous humor. Further studies may lead to useful conclusions for the role of zinc, copper, or cadmium in PEX syndrome.