Various problems on logistics systems have been dealt with recently as research issues since they were regarded critical for taking up a better position in the increasingly competitive global market. In particular, the freight transportation is considered as a key factor which affects the economic competitiveness of a whole nation as well as the production cost of individual companies. The objective of this study is to identify main issues and review recent foreign and domestic studies related to the freight transportation. The studies are classified into two categories according to the hierarchical level in the decision making process: infra structure design and transportation strategies, service design and operation. Main issues are introduced with a brief review on the related literature and methodologies applied.