Recently, two conflicting demands have arisen concerning research results of public research institutions. These institutions are mainly represented by universities, academies of sciences and other public scientific institutions. First, there is a growing pressure from the part of the public granting institutions, currently struggling with budget restrictions due to the economic crisis, to carry out research co-financed by the private sector (e.g. cooperation in applied research). For example, the European Union, represented mainly by the European Commission and national funding agencies are strengthening their demands for cooperation with private partners. However, legal limitations of a larger cooperation between public research institutions and private partners are becoming more and more obvious. These limitations can be seen, among others, in demands for research results being made more accessible (Open Access and Open Data), in rules for public aid policy, in diverging interests of public and private partners involved in joint research projects, in legitimate principles of free access to information, in the mixture of various legal systems, laws and rules (e.g. national, EU, international and bilateral agreements, rules of granting agencies, policy of collaborating companies), etc. This paper deals especially with the issue of results of applied research cooperation. It focuses on current legal problems concerning the software developed thanks to the cooperation of public research bodies and private companies.