Interdisciplinarity is becoming a central theme for discussion among researches and educators, renewing the enthusiasm of those who engaged in the past in non-reductionist, non-fragmentary epistemologies. On the graduate level, implementing and consolidating an interdisciplinary program is not an easy task. Institutional and cultural barriers constitute permanent challenges to be overcome. In this article, we present the history of 10 years of experience constructing the Interdisciplinary Post-Graduate Program on Agroecosystems at the Federal University of Santa Catarina, Brazil (PGA/UFSC). The process involved a constant effort to overcome adversities, which, on the one hand, made more difficult the consolidation of the program, but, on the other, promoted a rich environment for the intellectual growth of both the staff and the students. As with the concept and significance of interdisciplinarity, which is being constantly constructed, the debate over the nature, format and evaluation of “multidisciplinary” programs must be permanent. In contributing to this on-going debate, the PGA has a lot of accumulated experience, and, given the opportunity, it can help build a new graduate-level education project that seeks to transform all of those interested and that avoids viewing science as an end unto itself.