The article presents the results of the practical implementation of the methodology for assessing the innovative potential of small and medium-sized businesses of the Republic of Kazakhstan. To identify the level of development of innovative activity of SMEs in Kazakhstan the methods of correlation and regression analysis were implemented. The analysis conducted on the basis of available statistical materials disclosures the impact of different factors on the innovative potential of small and medium-sized businesses. According to the author's approach to the evaluation of innovative potential, there are three groups of factors affecting the innovative potential – factors of general economic development, factors of development of small and medium-sized businesses and factors of development of research activities. The article also analyzes the main indicators of innovation activity of the considered enterprises and institutional features of their development. The results of the research allowed to identify both the advantages and disadvantages of innovative activity of national SMEs.