One of the core problems in intensity modulated radiation therapy (IMRT) treatment planning is the fluence map optimization (FMO) problem, which determines a fluence map (or profile) for each beam used in the delivery of treatment. Radiation therapy is administered in multiple so-called daily fractions to allow for healthy tissue to recover from damage caused by the treatment. Before the advent of IMRT, the treatment was designed to ensure a constant dose to cells in the target (the areas in the patient where cancerous cells are present or suspected). In the presence of multiple targets with different prescribed doses, this design meant that treatment had to be delivered in a sequence of unequal fractions, one per prescription dose level. For example, in case of two targets treatment would consist of an initial plan aimed at treating both targets to a lower total dose, followed by a so-called boost plan aimed at delivering the additional dose at the target with higher prescribed dose. In contrast, IMRT treatment plans are often delivered with equal treatment plan for each fraction, which means that the dose per fraction cannot be the same for all targets. The important problem of restoring traditional fractionation to IMRT treatments has not yet received much attention in the literature. In this paper we propose a new optimization model that explicitly restores fractionation into the FMO problem, yielding an optimal set of fluence maps for each fraction. We illustrate the capabilities of our approach on clinical head-and-neck cancer cases. © 2013 Springer-Verlag Berlin Heidelberg.