Purpose - The purpose of this paper is to describe new methods to manage variation in complex manufacturing process chains and to show synergies between the variation risk management (VRM) and six-sigma approaches. Design/methodology/approach - The research methodology was experimental prototyping conducted in collaboration with industry partners. A prototype IT system was developed and tested to implement the approach. A quality cost-based system was used to assess variation at each operation stage, for every product characteristic. Findings - A comprehensive approach to the management of manufacturing variation is introduced, based on a new process risk matrix which can be used to specify an individual variation risk for every manufactured characteristic, throughout a manufacturing process chain. The approach has been implemented in a prototype software system and is aimed at the complex products such as those manufactured by the aerospace industry. Research limitations/implications - The IT approach described was developed during the research and is not commercially available. Practical implications - Manufacturing industry should be able to use this approach, in particular the process risk matrix concept, to develop more effective management of product variation and resultant cost, in complex process chains. Originality/value - The paper describes a novel approach to combine VRM and six-sigma concepts, and introduces the process risk matrix as a structure to understand process variation.