One of the strategic goals of the tax and custom administrations of the Baltic countries is to increase the efficiency and effectiveness in the use of resources. Therefore these countries are constantly looking for the solutions aimed at simplification of the administrative procedures, improvement and development of the service quality and the business environment in general, automatization of the internal work processes as well as significant reduction of the amount of manual work. This purpose of this publication is to provide the critical points of contact which are common for the three Baltic countries and to highlight the important differences that do not allow to perform an objective comparison of the three countries with regard to their tax and custom administration and combating crime. The novelty of this research – to offer a model for assessing the effectiveness of the tax and custom administrations of the Baltic countries, which is based on the factors influencing their efficiency and their relative importance.