Thermoeconomic methodologies represent a powerful tool for the energy system diagnosis when detecting possible malfunctions, localizing them and expressing their effects on the components in terms of thermodynamic and economic quantities. In this article, the role played by the control system in the propagation of malfunctions is analyzed. Its effects are proven to be relevant when the thermoeconomic diagnosis is performed and quantified for a gas turbine based cogeneration plant. (C) 2003 Published by Elsevier Ltd.