The Ministry of Education, Youth and Sports (MEYS) financially supports the Czech higher education institutions (HEIs). The largest amount of the MEYS's budget intended for HEIs subsidizes the public HEIs. Therefore, the aim of this paper is to measure the efficiency of the public higher education institutions. This will help us to determine which public HEIs can handle the sources (inputs) efficiently and how much the inefficient public HEIs should change their outputs to become efficient. We measure their teaching efficiency using data from 2015 and the DEA methodology. We run two analyses. The first analysis compares all the HEIs with each other. It shows that we have to consider the specialization of the HEIs. The second analysis divides the HEIs into three groups using coefficients of economic difficulties. This analysis shows that dividing the HEIs into groups helps us to eliminate the large differences in inputs and outputs. Therefore, we obtain better information about the efficiency of the HEIs.