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The paper addresses the complex issue of specialized audit of transport and logistics systems, a mandatory element of the Deming cycle of improving the quality of services. The general methodological bases for the audit of transport and logistics systems have been developed. The audit procedure of the public transport systems, consisting of eight basic components, as well as the practice of its application in order to improve the activity of the public transport system of Chisinau municipality is fully exposed. The system of quantitative and, respectively, qualitative indicators for assessing the quality of public transport services was developed. The practice of applying specialized audit confirms the importance of this method of improving transport and logistics systems.