Emission generated by the international merchant fleet has been suggested to represent a significant contribution to the global anthropogenic emissions. To analyze the impacts of these emissions, we present detailed model studies of the changes in atmospheric composition of pollutants and greenhouse compounds due to emissions from cargo and passenger ships in international trade. Global emission inventories of NOx, SO2, CO, CO2, and volatile organic compounds (VOC) are developed by a bottom-up approach combining ship-type specific engine emission modeling, oil cargo VOC vapor modeling, alternative global distribution methods, and ship operation data. Calculated bunker fuel consumption is found in agreement with international sales statistics. The Automated Mutual-assistance Vessel Rescue system (AMVER) data set is found to best reflect the distributions of cargo ships in international trade. A method based on the relative reporting frequency weighted by the ship size for each vessel type is recommended. We have exploited this modeled ship emissions inventory to estimate perturbations of the global distribution of ozone, methane, sulfate, and nitrogen compounds using a global 3-D chemical transport model with interactive ozone and sulfate chemistry. Ozone perturbations are highly nonlinear, being most efficient in regions of low background pollution. Different data sets (e.g., AMVER, The Comprehensive Ocean-Atmosphere Data Set (COADS)) lead to highly different regional perturbations. A maximum ozone perturbation of approximately 12 ppbv is obtained in the North Atlantic and in the North Pacific during summer months. Global average sulfate loading increases with 2.9%, while the increase is significantly larger over parts of western Europe (up to 8%). In contrast to the AMVER data, the COADS data give particularly large enhancements over the North Atlantic. Ship emissions reduce methane lifetime by approximately 5%. CO2 and O3 give positive radiative forcing (RF), and CH4 and sulfate give negative forcing. The total RF is small (0.01–0.02 W/m2) and connected with large uncertainties. Increase in acidification is 3–10% in certain coastal areas. The approach presented here is clearly useful for characterizing the present impact of ship emission and will be valuable for assessing the potential effect of various emission-control options.