Small and medium-sized enterprises (SMEs) are an essential part of every country's economic system. The quality of the business environment plays an important role in this regard. The aim of the paper was to define and quantify important public sector factors influencing the quality of the business environment in the SME segment and to compare the intensity of the defined factors between the Czech Republic (CR) and the Slovak Republic (SR). In regards to the defined aim, a survey-based research was conducted with enterprises operating in the SME segment. 312 enterprises in CR and 329 enterprises in SR were approached during this research. The scientific hypotheses were verified using the methods of Pearson statistics. The evaluation of political factors is quite negative in both countries. Only 15% of Czech and 20% of Slovak entrepreneurs positively evaluated the level of legislation in business. Both Czech and Slovak entrepreneurs see state's support of export quite positively. Only 12% of Czech and 22% of Slovak entrepreneurs positively evaluated the administrative burden on enterprises. Entrepreneurs in both countries claim that the state is unable to provide qualified workforce for businesses. Most significant differences between the two countries were found in the evaluation of state bureaucracy which the Slovak entrepreneurs evaluated more positively than their Czech counterparts. The results of the research show the need to deal with urgent issues, or create a better system of public factors influencing the business environment.