The article deals with multi-criteria performance measurement of innovative companies. As a tool for evaluating the performance of companies, a two-stage Data Envelopment Analysis (further DEA) is used. In the first stage of the analysis, effectiveness in terms of the protection of industrial property rights is quantified. In the second stage, efficiency, that means whether companies can commercialize industrial rights, is measured. The overall performance score, then, integrates both dimensions; efficiency and effectiveness. The article is divided into three consecutive parts, In the first part, the definition and measurement of performance of companies is discussed. Further, the DEA method is presented in more detail. The history of this method and its application in practice is briefly introduced. In the second part, the methodology used in the research and the data used are presented. The third part shows the results. The proposed methodology for evaluating the performance of innovative companies was tested on a sample of 36 innovative companies in the textile industry. To quantify individual performance components, the BCC input-oriented model was used because decreasing returns to scale in the industry were identified A long-term capital and the period of a company's existence as a measure of intellectual capital were used as inputs of the first model. The outputs of the first model are numbers of registered results of technical creative activity and industrial design. These outputs are also inputs to the second model. The output of the second model is the value added indicating whether the companies are able to commercialize protected industrial rights. At the end of the analysis, the companies are divided into four quadrants according to scores of effectiveness, efficiency and performance.