Objective of this study is to compare glass ionomer cement application and incus interpositioning techniques in patients who have chronic otitis media, conductive hearing loss with intact tympanic membrane and who undergo hearing reconstruction of staged surgery using a retrospective chart review in the setting of Ministry of Health Ankara Training and Research Hospital ENT Clinic, Turkey. We retrospectively evaluated patients who underwent otological surgery and hearing reconstruction with auto graft incus during 2005-2008 or glass ionomer cement during 2008-2010. Patients who had cholesteatoma, stapes fixation and tympanosclerosis were excluded. Postoperative mean follow-up time of 107 patients was 9.8 months (6-38 months, 83.2 % of them was ≤ 9 months). Postoperative pure tone hearing thresholds, graft status, gain scores and air bone gaps were recorded. Intact graft, dry ear on the operated side and ABG scores less than 20 dB were accepted as surgical success. Preoperative ABG score was 30.6 ± 7.93 dB in glass ionomer (group I) and 33.6 ± 11.99 dB in incus interpositioning (group II). Postoperative ABG scores were 13.6 ± 10.40 and 22.6 ± 12.39 dB, respectively, in group I and II. Success of closure in ABG scores was obtained in both groups (p < 0.001). Gain scores in group I were better (p = 0.035). Graft success (p = 0.020) correlated with gain score. Results showed that the glass ionomer cement application is a good, cost-effective technique, easy to perform and yields better hearing scores and lower complication rates compared to incus interpositioning technique.