Emissions from ships have recently received more attention since they have become a significant concern for air quality in harbours and port cities. This paper presents the methodology for a comprehensive maritime transport database of activity data, specific energy consumption, emission factors, and total emissions that have been developed within the European EX-TREMIS project. The model is built upon 3 modules: the fleet module, the transport activity module, and the emission module. The fleet module defines the ship categories, the loading capacities, and the engine characteristics of the different vessels by using EUROSTAT data, Sea Web Lloyd's database, and international literature. The transport activity module transforms total cargo handled (mainly based on EUROSTAT data and CEMT statistics) into ship-equivalents. These ship-equivalents are further transformed into ship-hours. The emission module calculates energy uses and CO(2), NO(X), SO(2), CO, HC, CH(4), NMHC, PM emissions from the resulting maritime activities. We have used technology based emission factors to take into account the technological evolution of vessels. To illustrate this new methodology, we present some results (emissions, fuel consumption and emission factors) for different countries. The overall methodology as well as the results and the country specific energy consumption and emission factors per ship type and size class can be extracted from the EX-TREMIS website (www.ex-tremis.eu). Our results contribute to more accurate estimates of emissions and air quality assessments in coastal cities and ports.