The aim of this paper is to present the issues of funding of science and research in the Czech Republic for consideration. Most financial resources for science and research stem from the state budget and EU structural funds. In order to improve the distribution of these funds specific criteria and methods used for the efficient allocation of resources are selected. To determine the criteria the method of gradual schedule of weights and the significance criteria method compared with their preferential order is used. To unify criteria values the method of linear partial utility functions is used. Application of these methods is focused on targeted support to address individual projects, namely the allocation of grants. The output of this evaluation is appropriate for the state body in charge of distribution of science and research financing.