Boundary crossing in undergraduate and graduate learning environments is still a relatively unstudied phenomenon, at least in comparison with the attention given to studies of interdisciplinary research. The research reported here focuses on learning environments in the context of Swedish higher education and is based on interviews and fieldwork at two interdisciplinary programs at two universities. The main findings are summarized in twelve themes which represent different ways of understanding the complexity of boundary crossing in pedagogical practice. We identify the shifting conjunctures of higher education in which key notions such as boundary crossing can demonstrate a strong attraction as well as its opposites in the form of strong rejection.