The thermoeconomic diagnosis strategy introduced in the accompanying paper [Verda, V, Serra, L., Valero, A. 2004. Thermoeconomic Diagnosis: Zooming Strategy Applied to Highly Complex Energy Systems. Part 1: Detection and Localization of Anomalies. Part 1: The diagnosis procedure. ASME J. Energy Resour Technol. 127(1), pp. 42-49. This issue.] is a zooming technique consisting of a successive localization of anomalies. At each step the required productive structure to be adopted becomes even more detailed, focusing the analysis on a more specific part of the system. The detail of a productive structure has two different levels: the number of components and the number of productive flows. The first one is selected according to the precision desired in locating the anomalies. A larger number of components (or subsystems) allows one to locate the anomalies in smaller control volumes, providing more precise indications for maintenance. The number of flows is partially dependent on the number of components. Once the number of components is fixed, the productive flows can be increased by separating exergy into its components or introducing fictitious flows, such as negentropy (see, for example, C. A. Frangopoulos, Energy The International Journal 12(7), pp. 563-571 (1987)). This decision also affects the results of the thermoeconomic analysis when it is adopted for diagnosis purposes. In this paper, the effects of the productive structure on the diagnosis results are carefully analyzed. Depending on the selected productive structure, the accuracy of the diagnosis results can be significantly improved.