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To assess aqueous flare as a measure of subclinical inflammation after Descemet membrane endothelial keratoplasty (DMEK) for Fuchs endothelial dystrophy.In this prospective cross-sectional and longitudinal case series at a tertiary referral center, 173 DMEK eyes of 169 patients and 19 age-matched healthy control eyes were included. Aqueous flare [photon count per millisecond (ph/ms)] was assessed by laser flare photometry at 1 day, 1 week, and 1 month after DMEK in group I (evaluation of postsurgical blood–aqueous barrier recovery; n = 25) and on average 28 (±19) months (range, 3–86 months) after DMEK in group II (evaluation of long-term inflammation; n = 148).In group I, flare levels decreased from 1 day to 1 week [25.1 (±9.1) ph/ms vs. 13.4 (±4.8) ph/ms; P = 0.003] and remained stable up to 1 month after DMEK [12.1 (±3.2) ph/ms; P = 0.387]. However, average flare at 1 month was higher than that in healthy controls (P < 0.001). The long-term flare value after DMEK (group II) was 9.6 (±4.2) ph/ms and was higher in eyes associated with allograft rejection (n = 6) versus those without rejection [16.7 (±7.8) ph/ms vs. 9.3 (±3.8) ph/ms, respectively, P < 0.001]. All eyes associated with rejection had flare values above 10 ph/ms.Aqueous flare after DMEK quickly decreased within the first postoperative month, indicating fast recovery of the blood–aqueous barrier. Long-term flare levels were higher in eyes associated with rejection, suggesting persistent subclinical inflammation. A flare level above 10 ph/ms may be used as a threshold for identifying eyes associated with or at risk of allograft rejection after DMEK.