This paper aimed to analyze the factors that influence the choice of governance structures in the sugarcane agroindustry of Paraná There were analyzed by the New Institutional Economics (NIE), the characteristics of the transactions and the agents in two agro-industries. Data collection was carried out through interviews and correspondence with representatives of agroindustries and the State of Paraná Bioenergy Producers Association (ALCOPAR), bibliographic and documentary research. In transactions of cultivation, harvesting and transportation of cane, Alfa agroindustry verticalizes, while Beta agroindustry adopts contract with intervention, verticalization and simple contract, respectively. For the purchase of industrial inputs both choose to market or simple contracts, and the labor contract, both opt for CLT regime. In commercialization and transportation transactions of sugar and ethanol, Alfa uses the market, simple contracts and cooperation (CPA Trading) and Beta uses cooperation.For the production and sale of electricity, Alfa verticalizes and Beta has a partnership agreement. Uncertainty and bounded rationality were the most relevant factors in the choice of governance structures by Alfa, to Beta was cooperativism. Asset specificity, frequency and uncertainty influenced governance structures adopted in the analyzed agricultural industries, mainly in the supply of raw materials; reputation had slight influence.