Diesel engines are the most efficient combustion engines today, playing an important role in transport of goods and passengers on land and on sea. The main drivers for the design of future engines is the control of the emissions without sacrificing their advanced fuel economy. These drivers led to important innovations in multiple components of the engine, which, however, complicated the nature of the processes taking place and increased the need for highly accurate simulation frameworks. In the current article, the focus is on the recent progress of combustion modeling of diesel engines. The major general challenges encountered are first introduced briefly and then the progress in various research areas is reported in more details. Special focus is given to the most commonly used combustion models describing their advantages as well as their shortcomings. In the end, some closing remarks are presented as guidelines for future modeling efforts.