This paper presents the theoretical roots from which emerges the New Institutional Economics (NIS). It shows that the NIS, in discussion with other branches institutionalists, reveals important theoretical limitations and contradictions. The lack of that rescue in studies on agribusiness prevents the observation of important issues of the Brazilian agribusiness, such as conflict, power and culture in the formation of structures of governance. The paper presents, first, the link between the understanding agribusiness in its systemic form and the institutionalist thought. Then, recovers the sources and branches of Institutional Economics, and shows that NIS is linked to the methodological individualism, which differs from the original institutionalism. It is concluded that the NIS is limited theoretical framework to understand the structures of governance observed in Brazil, mainly in the Brazilian agribusiness.