This paper investigates how freight rates paid by shippers are affected by the characteristics of urban areas of origin and destination. It is based on a commodity flow survey between 45 Japanese prefectures from 2000 to 2010. Through an analysis of freight rates, authors seek to identify the advantages and disadvantages faced by shippers depending on the spatial arrangement of their freight flows. The results show that shipping cargo from small to large urban areas is less costly than in the reverse direction, other things being equal. This difference may be due to the higher probability for truck companies to find back-haul cargo when the destination is a large urban area, usually involving a larger truck transport market. Another important finding of this study is that intra-urban freight rates are positively correlated with population size. The latter may result from higher levels of congestion, labour costs, weight and size restrictions on vehicles, as well as higher proportions of light goods such parcels and courier flows.