Purpose: This article aims to show the linkage of Iranian agricultural research centres with extension and farmers, using three case studies in 1999, 2005 and 2010. Design/methodology/approach: The data were collected through document analyses, structured and semi-structured interviews and observations. Findings: The 1999 and 2005 cases were conducted in a context in which both extension services and research centres were publicly funded and managed by the Ministry of Agriculture. In this period, some extension-research linkage mechanisms were defined, such as providing incentives to researchers to define their research projects based on farmers' needs, joint publications, joint on-farm research and joint meetings. Despite these regulations, poor knowledge management among social actors led to a disciplinary orientation for most researchers and their poor relationship with farmers and extensionists. They also tended to have a negative attitude towards farmer-oriented participatory research approaches. In the mid 2000s, government ratified legislation to privatize the extension system. The case study from the 2010s revealed that agricultural researchers had little connection with private agricultural services delivery companies. Practical implications: No particular mechanism has been developed to link research centres to the private sector. The researchers have been encouraged to focus on the research problems which are mostly based on academic incentives, rather than farmers' needs. The privatization has led to a poorer linkage of research with extension systems and farmers. Originality/value: The originality of this study lies in the importance of the collaboration of agricultural research, extension and farmers in agricultural innovation systems. This research also contributes to the pluralistic concepts of extension systems and the consequences of privatization. (Contains 4 figures, 1 table and 1 note.)