The article presents the survey results of obstacles to small innovative companies as a case study of Nizhny Novgorod region of Russia as an area with high innovative potential and great level of socio-economic indicators. Based on the semi-structural personal interviews with 19 experts - the management of support infrastructure, results shows some typical for this region impediments: bureaucracy; lack of trust, poor collaboration within the innovation system; poor information support; legislative obstacles to innovations and intellectual property protection; low interest of large companies in collaboration with small ones. The findings and recommendations can help policy-makers to meet the needs of small innovative companies, and increase the innovative activity of small firms through the improvement of the assistance programs.