Assessing nuclear energy transition scenarios requires appropriate modelling tools. The IAEA tool, Model for Energy Supply System Alternatives and their General Environmental Impacts (MESSAGE), is described in this publication. The tool simulates the development of a complete energy system and provides a convenient platform for modelling and analysing nuclear energy systems (NESs), as it can efficiently model nuclear technologies with their specific features. Among other things, the tool can help produce a description of an entire NES with time dependent parameters for long-term planning; confirm the feasibility of a NES through correlation and consistency of all NES components, taking into account all constraints and boundary conditions imposed on the system; and balance fissile material in a closed fuel cycle and determine fuel cycle requirements. In addition, it assists the user in the choice of alternatives by comparison of different options relating to fuel requirements and volume and toxicity of waste. The publication provides a detailed guidance on how to build mathematical models representing complex nuclear energy systems within the framework of the MESSAGE tool.