Although the concept of holonic manufacturing systems (HMS) has been proposed for over a decade, several desired properties of HMS such as fault tolerance have not been quantitatively characterized and rigorously proven. This paper aims to provide a theoretical foundation for analyzing the fault tolerant properties of holonic assembly/disassembly processes in HMS. Fault tolerant analysis is concerned with the impact of resource failures on the operation and performance of HMS. The goal of fault tolerant analysis is to Study the ability to retain the operation of holonic processes in the presence of resource failures. To study fault tolerant properties, we propose a collaborative Petri net (CPN) to model holonic assembly/disassembly processes and formulate an optimization problem to minimize the cost of CPN. We propose a greedy algorithm to find a nominal optimal solution. Based on the nominal Solution, we analyze the effects of resource failures on the operation and performance of the holonic assembly/disassembly processes. Computational complexities are also analyzed. (C) 2008 Elsevier Ltd. All rights reserved.