In the context of globalisation of economic relationships, intensification of transportation and technological solutions, the methodology of research and development of transport infrastructure requires improvement and adaptation to dynamically changing conditions of the transportation market.The objective of the work is to formalise and to develop a methodology for studying transport infrastructure, including specialised isothermal rolling stock. The initial data on cargo turnover were processed by the methods of mathematical statistics, and the technical parameters of innovative isothermal rolling stock were substantiated using the methods of T. Saaty analytic hierarchy process, expert assessment, and update engineering design process.The article provides an analysis of the cargo turnover of perishable goods transported by railway refrigerated transport in Russia in terms of volumes, types of rolling stock, and origin. The main origin-destination cargo flows are presented by types of transportation (domestic, transit, export, import transport operations). It has been determined that key factors in development of isothermal rolling stock for transportation of perishable goods in the transport system of the country refer to transportation of meat, fish, beer, soft drinks, juices in the segment of domestic transportation. The analysis shows that there are no structural and quantitative shifts in terms of types of transportation and types of cargo.The strategy for development of vehicles for transportation of perishable goods and the methodology are presented in a block diagram, in sections: «statement of the research problem», «decision-making stages», «decision implementation methods and algorithms». It is shown that the problem includes not only development of stationary railway infrastructure and of stages in development of isothermal rolling stock, but also the need to solve organisational, technical, technological, regulatory, and legal problems, as well as tariff regulation.The issues of methodology for designing an innovative isothermal rolling stock are considered referring to possible prospects for its development and areas of operation, as well as to a set of engineering and technological solutions. The study of linear dimensions and useful section of the loading space of various types of isothermal bodies shows the advantage of wagons and swap bodies in comparison with large-capacity refrigerated containers.It is proposed to design a prototype of innovative isothermal rolling stock on the basis of a universal isothermal swap body, configured with various types of refrigerating equipment with specified technical parameters that best meet the requirements of the modern transportation market. The areas of possible use of various types of isothermal rolling stock are analysed considering long-term forecasts for development of agricultural, fishing and processing industries.