This paper presents an analysis on the links among universities and public research institutes with the industry in Costa Rica. The study analyses information from three different sources. The first one is a data base from the national survey of science, technology and innovation in Costa Rica. The other one is a survey to researches in universities and public research centres. A third source is a deep interview to researchers within universities and public research centres. The objective of the study is to have a better understanding of the creation, transfer and materialisation of knowledge in the innovation processes of the industry. The main results give us an idea of the weakness of the Costa Rican innovation system. There are clear difficulties for the universities and the public research centers to develop satisfactory links with firms. It is a high concentration of the investment in science and technology in the academic sector. It would be natural that firms have access to the efforts by research centers. However, it is obvious that the percentage of firms that has an effective linkage with the universities and public research centers is very low. Some institutional barriers and mistrust between these actors, avoid better linkages. But there are also some positive efforts. The study focuses on the elements that promote or hinder the linkage among universities and firms, and attend the challenges of developing economies to improve these kinds of relationships. A chain of limitations hinder useful interactions of universities and public research centres with the industry, hindering innovation processes by firms. Most of the barriers are internal problems to the research centres, including very bureaucratic processes that hinder the possibility to joint projects with firms. It seems natural to strengthen trust among universities, public research centres and firms, but also the introduction of institutional changes that facilitate networking.