The purpose of this work is to define safe irradiation protocols in microbeam radiation therapy. The intense synchrotron-generated x-ray beam used for the treatment is collimated and delivered in an array of 50 μm-sized rectangular fields with a centre-to-centre distance between microplanes of 400 μm. The absorbed doses received by the tumour and the healthy tissues in a human head phantom have been assessed by means of Monte Carlo simulations. The identification of safe dose limits is carried out by evaluating the maximum peak and valley doses achievable in the tumour while keeping the valley doses in the healthy tissues under tolerances. As the skull receives a significant fraction of the dose, the dose limits are referred to this tissue. Dose distributions with high spatial resolution are presented for various tumour positions, skull thicknesses and interbeam separations. Considering a unidirectional irradiation (field size of 2×2 cm2) and a centrally located tumour, the largest peak and valley doses achievable in the tumour are 55 Gy and 2.6 Gy, respectively. The corresponding maximum valley doses received by the skin, bone and healthy brain are 4 Gy, 14 Gy and 7 Gy (doses in one fraction), respectively, i.e. within tolerances (5% probability of complication within 5 years).