Aim of the present study was to evaluate the accuracy which can be obtained with helical TomoTherapy® (HT, Accuray) systems in the case of multiple intracranial targets treatments. Set-up accuracy was measured, for different registration options and MegaVoltage CT (MVCT) slice thickness, by applying known misalignments to an ad-hoc developed phantom. End-to-end (E2E) tests were performed to assess the delivery accuracy in phantoms containing multiple targets by using radiochromic films: measured dose distribution centroids were compared with physical and calculated target positions on axial and coronal planes. A Gamma index analysis was carried out on planned and measured planar dose maps. The bone and tissue algorithm with the fine MVCT reconstruction grid gave the best results among the automatic options. The most accurate registration modality resulted to be the manual one with a sub-voxel accuracy shifts and a capability in the detection of rotations within 0.3°. For the E2E along the coronal plane (six targets), a mean deviation between measured dose distribution centroids and physical barycenters of 0.6 mm (range 0.1 mm-1.3 mm) was observed. Along the axial plane (five targets), a mean deviation of 1.2 mm (range 0.7 mm-2.1 mm) was found for the centroids shifts. Gamma index (5%, 1 mm, local) passing rates higher than 87.5% between planned and delivered dose distributions were measured. These results demonstrate that multiple brain lesion HT treatments are feasible with an accuracy at least comparable to frameless linac-based delivery, when a set-up capable to assure angular corrections and a reliable patient immobilization is employed.