We estimate the effect of the Russian University excellence program (Project 5-100) initiated by the Government in 2013 on research performance of top Russian universities which received, on a competitive basis, substantial financial support within this program. To do so we use an econometric analysis of longitudinal data applying a linear growth model with mixed effects, with different characteristics of research output as dependent variables. We demonstrate that there is a significant positive effect of Project 5-100 which appeared from the very first years of its implementationthat is, the universities receiving financial support demonstrate a substantial, steady increase in publications both measured in total numbers and per capita when compared to universities from the control group. An analysis of the structure of publication output allows us to demonstrate that not only quantitative but also qualitative growth has taken place, although the impact of Project 5-100 on quality is heterogeneous across universities and disciplines. Finally, we examine to what extent the change in the structure of research output may be attributed to changes in research collaboration patterns.