In the paper is described, and applied in some case studies, a complete methodology for the estimate of air pollutant emissions fi om ships in port environment and in navigation. The following pollutants are take into account: Nitrogen oxides, Sulfur oxides, and Carbon monoxide, Volatile Organic Compounds, Particulate matter, Carbon dioxide. The paper introduces a schematic representation of ship traffic, from the point of view of consumption and emissions, subdividing the operation in: cruising, maneuvering, hotelling and tanker offloading. The emissions are estimated from daily fuel consumption, days spent in the different operations and average pollutants emission factors. The paper report regression formulas on fuel consumption at full power vs. gross tonnage (measured in line with the 1969 International tonnage convention) for each ship class and fraction of maximum fuel consumption in different operation mode. The following; classification of ships by type is used for fuel consumption evaluation: solid bulk, liquid bulk, general cargo, container, passenger/ro-ro/cargo, passenger, high speed ferries, inland cargo, sail ships, tugs, fishing, other. Default emission factors are introduced for steam engines, high speed motor engines, medium speed motel engines, slow speed motel engines, inboard pleasure engines, outboard engines, tanker offloading engines. Case studies of high Tyrrhenian Sea ports of Genoa, Savona, La Spezia, Imperia, Livorno, Marina di Carrara, Piombino and Portoferraio are discussed. The specific port studies has been realized in the frame of Regional Air Pollutant Management Plans.