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The paper presents the results of work being undertaken as part of the UK contribution to an International Energy Agency research project (Annex 34) concerned with computer-aided fault detection and diagnosis in real buildings. The aim of the project is to develop and test software tools, which are based on existing methods of fault detection and diagnosis, for analysing the performance of heating, ventilating and air-conditioning systems. The development of a tool, which can automate the commissioning of air-handling units in large-scale air-conditioning systems, is considered in this paper. The presence of faults is detected by a fuzzy model-based fault diagnosis scheme which uses generic reference models to describe the behaviour of the plant when it is operating correctly and when one of a predefined set of faults has occurred. The paper discusses practical issues such as the integration of the commissioning tool and the building energy management system, the automatic reconfiguration of the control strategy to implement open-loop commission tests, the automatic generation of the test sequences, and the presentation of the diagnostic results to the user. Experimental results are presented that demonstrate the use of the tool to remotely commission the cooling coil of an air-handling unit in a commercial office building.