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Agglutinative languages such as Turkish, Finnish andHungarian require morphological disambiguation beforefurther processing due to the complex morphologyof words. A morphological disambiguator is usedto select the correct morphological analysis of a word.Morphological disambiguation is important because itgenerally is one of the first steps of natural languageprocessing and its performance affects subsequent analyses.In this paper, we propose a system that uses deeplearning techniques for morphological disambiguation.Many of the state-of-the-art results in computer vision,speech recognition and natural language processinghave been obtained through deep learning models.However, applying deep learning techniques to morphologicallyrich languages is not well studied. In this work,while we focus on Turkish morphological disambiguationwe also present results for French and German inorder to show that the proposed architecture achieveshigh accuracy with no language-specific feature engineeringor additional resource. In the experiments, weachieve 84.12 , 88.35 and 93.78 morphological disambiguationaccuracy among the ambiguous words forTurkish, German and French respectively.