Multinomial logit models of firms’ choice of transport chain and shipment size are estimated for 16 commodity groups. The estimations are based on the Swedish Commodity Flow Survey (CFS) for 2016 and 2021 with choice data for individual shipments. The CFS is combined with cost and transport time data from the Swedish national freight transport model, Samgods, in order to estimate the impact of transport costs on firms’ transport chain and shipment size choice. Empirical midpoints of shipment sizes are included in the estimations such that the impact of ordering cost and holding cost are considered, which influences the transport cost estimates. Overall, results show that transport costs have a statistically significant impact on firm’s choice of transport, and the impact varies with respect to commodity group.