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This paper describes the historical development of indirect support in the Czech Republic and analyses the available data from the period 2005–2013. The aim of the research is to demonstrate a dependence between the introduction of a new type of support for research and development and the increase in investment in companies’ own R&D in the manufacturing after 2005. The objects of the research are all domestic concerns engaged in business that reported the financing of their own research by means of the deductible item for R&D. The number of concerns in individual branches of the manufacturing industry differs markedly, for which reason more-detailed analysis of individual branches did not comprise part of the investigation into the subject of this research. We used regression analysis to monitor the development of R&D expenditure in the manufacturing industry. Exponential regression was best suited to the estimation of non-linear parameters. By analysing secondary data, we discovered that the introduction of the deductible item in 2005 is acting as support for increasing companies’ own investment in R&D. The tax incentive is a method of financing a company’s own R&D that is being used increasingly often.