This thesis deals with the innovation of information system (IS) as a decision problem. The main objective of this thesis is the construction and the application of a method to select an optimal innovation variant of IS in an organisation of any scale. The designed method is based on the conception of the innovation of IS in the methodology "Multidimensional Management and Development of Information System (MMDIS)". The proposed selection method (Method of Innovation Modules based on MMDIS - MIM) is intended to serve mainly for decision-making on a strategic level. The IS structure is mapped in accordance with the MMDIS methodology. Innovation aspects are derived from two approaches: innovation aspects based on the MMDIS principles ("module...