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Calculation of external costs in ports is often based on the estimation of necessary input values. Such approach leads to the large differences between results of different researchers and does not show exactly the share of the individual polluter. Internalization of external costs as a tool of current European Union transport policy requires accurate data in order to realize the principle "polluter pays". Authors emphasize three main guidelines: air pollutant emission as a source of pollution, fixed number of people as an exposure to pollution and a certain way of interpretation of results. The calculation is based on values of emissions from ships rather than on values measured in air. Parameters for calculation are previously known from the ship registers, spreadsheets, and public documents, and only the fuel consumption measurement is desirable. The concept avoids the uncertainties in research as much as possible, enables identification of polluter and its share in total pollution, and could make valuation procedure more precise and fair.