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Abstract Background To evaluate clinical results in eyes undergoing phacoemulsification intraocular lens (IOL) implantation due to Fuchs, uveitis (FU) related complicated cataract. Methods Post-surgical outcomes of 56 eyes of 55 FU patients were evaluated retrospectively. Three groups were formed according to the IOL model: hydrophilic SAF6125 (Optima fold) acrylic, hydrophobic SN60AT (Alcon), and hydrophobic AAB00 (Abbott). Postoperative posterior capsular opacification (PCO) development and PCO development time, neodymium number: YAG laser posterior capsulotomy rate, giant cell (GC) deposition on the IOL, and the development time of GC deposits were compared among the groups. All patients were followed postoperatively on the 1st day, 1st week, 2nd and 6th weeks, and then at 3-month intervals. Results The hydrophilic SAF6125 IOL was implanted in 10 eyes, hydrophobic SN60AT in 24 eyes and AAB00 IOL in 22 eyes. The mean postoperative follow-up time was 34.1 ± 30.1 (6-144) months. PCO developed in 7 eyes (70%) in the hydrophilic SAF6125 group, 17 eyes (70.8%) in the hydrophobic SN60AT and 13 eyes (59.1%) in the AAB00 group. There was no statistically significant difference among the three IOL groups in the PCO development, the PCO development time and YAG laser capsulotomy rates (P = 0.674, P = 0.111, and P = 0.507, respectively). The PCO development time was significantly longer in the hydrophobic SN60AT than AAB00 group (P = 0.027). GC deposits were detected in 3 eyes (30%) in the hydrophilic SAF6125 group, 7 eyes (29.1%) in the hydrophobic SN60AT and 3 eyes (13.6%) in the AAB00 group. GC deposition and the development time of GC deposits were similar among the three IOL groups (P = 0.575, P = 0.804). At the final follow-up, BCVA was ≥ 20/40 in 41 eyes (73.2%). Conclusion The GC deposits and PCO development were the most important problems in these eyes with hydrophilic or hydrophobic IOLs despite good visual and postoperative results. New developments are needed in terms of IOL design or content in eyes with FU.