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This paper describes the MIT-LL/AFRL statistical MT system and the improvements that were developed during the IWSLT 2009 evaluation campaign. As part of these efforts, we experimented with a number of extensions to the standard phrase-based model that improve performance on the Arabic and Turkish to English translation tasks. We discuss the architecture of the MIT-LL/AFRL MT system, improvements over our 2008 system, and experiments we ran during the IWSLT-2009 evaluation. Specifically, we focus on 1) Cross-domain translation using MAP adaptation and unsupervised training, 2) Turkish morphological processing and translation, 3) improved Arabic morphology for MT preprocessing, and 4) system combination methods for machine translation.