In article given key questions of functioning of small innovation business at higher education institutions as one of the most important components of innovation technologies introduction from educational institutions into the market are considered. There are given the main negative tendencies of organizational and legal nature, which interfere with effective functioning of the small innovation enterprises created on the basis of higher education institution within the Federal law No. 217. Moreover, the problem of intellectual property management and commercialization in terms of innovation activity of higher education institution is considered, and also recommendations on its elimination are offered in the article.