Developments in Holonic Manufacturing Systems (HMS) have been reported in three main areas: architectures, algorithms, and methodologies for HMS. Despite the advancements obtained in the first two areas the methodologies for HMS have not received great attention. To date, many of the developments in HMS have been conducted in an almost “empirical way”, without design methodology. There is a definite need to have methodologies for HMS that can assist the system designer at every development steps. This methodology should also provide clear and unambiguous analysis and design guidelines. To this end, in this work we present a Multi Agent Methodology for HMS analysis and design.