Purpose: To assess the effects of brain movements induced by heartbeat on dose distributions in synchrotron micro- and mini-beam radiaton therapy and to develop a model to help guide decisions and planning for future clinical trials. Methods: The Monte Carlo code PENELOPE was used to simulate the irradiation of a human head phantom with a variety of micro- and mini-beam arrays, with beams narrower than 100mum and above 500mum, respectively, and with radiation fields of 1cmx2cm and 2cmx2cm. The dose in the phantom due to these beams was calculated by superposing the dose profiles obtained for a single beam of 1mumx2cm. A parameter delta, accounting for the total displacement of the brain during the irradiation and due to the cardio-synchronous pulsation, was used to quantify the impact on peak-to-valley dose ratios and the full-width at half-maximum. Results: The difference between the maximum (at the phantom entrance) and the minimum (at the phantom exit) values of the peak-to-valley dose ratio reduces when the parameter $delta$ increases. The full-width at half-maximum remains almost constant with depth for any $delta$ value. Sudden changes in the two quantities are observed at the interfaces between the various tissues (brain, skull and skin) present in the head phantom. The peak-to-valley dose ratio at the center of the head phantom reduces when delta increases, remaining above 70% of the static value only for mini-beams and delta smaller than ~200mum. Conclusions: Optimal setups for brain treatments with synchrotron radiation micro- and mini-beam combs depend on the brain displacement due to cardio-synchronous pulsation. Peak-to-valley dose ratios larger than 90% of the maximum values obtained in the static case occur only for mini-beams and relatively large dose rates.