This study considers the relationship between the size of the firm and innovation policy. The study includes a joint analysis of distribution and the effect of R&D subsidies on inputs and outputs of the innovation process of small and medium enterprises (SMEs) and large firms. Although size has a significant, positive influence on firms’ propensity to obtain R&D subsidies, large firms do not always show the strongest effects and in some cases such an effect is not significant. The study likewise concludes that subsidies are effective in increasing the inputs to the innovation process of SMEs and the outputs of large firms. One must consider these differences when evaluating and designing future innovation policies.