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Purpose Cytokine patterns in the aqueous humor before penetrating keratoplasty might permit us to predict the development of immune reactions. We therefore analyzed ten different cytokines in the aqueous humor of patients before and following penetrating keratoplasty. Methods We collected aqueous humor from patients undergoing cataract extraction or penetrating keratoplasty (baseline, n=197), from patients undergoing cataract extraction after penetrating keratoplasty without signs of an endothelial immune reaction (acceptors, n=33), and from patients who underwent irrigation of the anterior chamber due to endothelial immune reactions (rejectors, n=25). We determined interleukin (IL)-1b, IL-2, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, interferon (INF)-γ, and tumor necrosis factor-α in the aqueous humor, using cytometric bead arrays. Results We found statistically significant differences for IL-10 and INF-γ among the study groups. We observed no significant differences concerning all other cytokines evaluated in this study. Conclusions Elevated levels of INF-γ emphasize its important role in immune reactions following penetrating keratoplasty. Antagonizing INF-γ might be an option when treating immune reactions. High levels of IL-10 during endothelial immune reactions may reflect a downregulation of the delayed-type hypersensitivity. Perhaps this is a donor-specific activation of the immune privilege in the anterior chamber as an attempt to prevent damage during immune reactions. We plan to investigate, in upcoming prospective trials, whether the analysis of cytokine patterns in the aqueous humor before penetrating keratoplasty will enable us to predict the occurrence of immune reactions.