Uyghur is one of the Turkic languages in the Altaic language family. We are developing a machine translation system to translate from English into Uyghur. As there are no previous researches devoted to machine translation between English and Uyghur and being short of related works that we could use as a base for our research, we noted that by making clear the morphological and syntactic similarities and differences between Japanese and Uyghur we can make use of the approaches and methods of English-Japanese machine translation to make faster progress in our research. In order to attain this goal, we have performed a comparative study on the Japanese and Uyghur grammars. In this paper, we describe the similarities as well as differences between Japanese and Uyghur in both levels of morphology and syntax and we give a brief description of our English-Uyghur transfer method to which we are aiming at applying our comparative study on Japanese and Uyghur grammars.