OBJECTIVE Selenium supplementation was seen to be linked to glaucoma disease in a previous study (Lillico A. JE, Reid M et al. (2002) Selenium Supplementation and Risk of Glaucoma in the NPC trial University of Arizona, Tucson, AZ., Arizona Cancer Center). As aqueous humor levels of selenium seemed to be associated with primary open-angle glaucoma (POAG), the aim of this study was to analyze concentrations of selenium in aqueous humor samples of patients with POAG and pseudoexfoliation glaucoma (PEXG) in comparison to normal samples. METHODS Thirty-eight aqueous humor samples from patients undergoing cataract surgery were collected: Eleven patients with PEXG (age 65.8 ± 10.69, female 6, male 5), 12 patients with POAG (age 65.3 ± 10.50, female 7, male 5) and 15 patients without glaucoma (age 70.9 ± 12.83, female 10, male 5, controls). Aqueous humor levels of selenium were measured by Flow-Injection-Inductively-Coupled-Plasma-DRC-Mass-Spectrometry (ICP-DRC-MS). RESULTS Maximum likelihood estimation of the least squares means (LS-means) and the relative 95% confidence limits of selenium aqueous humor levels were 6.90 ± 1.03 μg/L (control), 6.74 ± 1.14 μg/L (POAG) and 8.25 ± 1.18 μg/L (PEXG). The data were modeled using a generalized linear model (GLM) analysis, where selenium was set as dependent variable. The model was corrected for group differences in age and gender. The data show no differences among all the calculated differences between the least square means (LS means), taking in consideration the simultaneous 95% confidence limit and the multiple comparison tests with Tukey-Cramer adjustment. The evaluation of the model disclosed that POAG and PEXG patients had no significantly different aqueous humor selenium concentrations compared to controls and to each other. However, the quantile regression analysis of selenium aqueous humor levels showed differences in quantiles for open-angle glaucoma patients considering age and gender. CONCLUSIONS As no significant difference in aqueous humor concentration of selenium was detected between open-angle glaucoma and controls, however, quantile analysis showed differences in quantiles levels for different age ranges in open-angle glaucoma patients, the trace element selenium seemed to be linked to glaucoma disease, yet not in a major role.