Abstract Background and purpose: The dose due to secondary neutrons and photons in proton therapy was estimated with Monte Carlo simulations. Three existing facilities treating eye and deep-seated tumours were taken into account. The results of the calculations related to eye proton therapy were verified with measurements. Materials and methods: The simulations were performed with the FLUKA code. Neutron fluence was measured inside an Alderson phantom (type ART) with activation techniques. Results: The maximum dose due to secondaries produced in a passive beam delivery system was estimated to be of the order of 10 −4 and 10 −2 Gy per therapy Gy for eye and deep tumour treatments, respectively. In the case of irradiations of deep-seated tumours carried out with an active system, the dose was of the order of 10 −3 Gy per therapy Gy. Conclusions: The dose due to secondaries depends on the geometry of the beam delivery system and on the energy of the primary beam and is lower in the healthy tissues distant from the target volume.