Purpose:To calculate absorbed doses due to neutrons in 87 organs/tissues for anthropomorphic phantoms, irradiated in position supine (head first into the gantry) with orientations anteroposterior (AP) and right–left (RLAT) with a 18 MV accelerator. Conversion factors from monitor units to μGy per neutron in organs, equivalent doses in organs/tissues, and effective doses, which permit to quantify stochastic risks, are estimated.Methods:MAX06 and FAX06 phantoms were modeled with MCNPX and irradiated with a 18 MV Varian Clinac 2100C/D accelerator whose geometry included a multileaf collimator. Two actual fields of a pelvic treatment were simulated using electron–photon–neutron coupled transport. Absorbed doses due to neutrons were estimated from kerma. Equivalent doses were estimated using the radiation weighting factor corresponding to an average incident neutron energy 0.47 MeV. Statistical uncertainties associated to absorbed doses, as calculated by MCNPX, were also obtained.Results:Largest doses were absorbed in shallowest (with respect to the neutron pathway) organs. In , values of 2.66 (for penis) and 2.33 (for testes) were found in MAX06, and 1.68 (for breasts), 1.05 (for lenses of eyes), and 0.94 (for sublingual salivary glands) in FAX06, in AP orientation. In RLAT, the largest doses were found for bone tissues (leg) just at the entrance of the beam in the body (right side in our case). Values, in , of 1.09 in upper leg bone right spongiosa, for MAX06, and 0.63 in mandible spongiosa, for FAX06, were found. Except for gonads, liver, and stomach wall, equivalent doses found for FAX06 were, in both orientations, higher than for MAX06. Equivalent doses in AP are higher than in RLAT for all organs/tissues other than brain and liver. Effective doses of 12.6 and 4.1 were found for AP and RLAT, respectively. The organs/tissues with larger relative contributions to the effective dose were testes and breasts, in AP, and breasts and red marrow, in RLAT. Equivalent and effective doses obtained for MAX06/FAX06 were smaller (between 2 and 20 times) than those quoted for the mathematical phantoms ADAM/EVA in ICRP‐74.Conclusions:The new calculations of conversion coefficients for neutron irradiation in AP and RLAT irradiation geometries show a reduction in the values of effective dose by factors 7 (AP) and 6 (RLAT) with respect to the old data obtained with mathematical phantoms. The existence of tissues or anatomical regions with maximum absorbed doses, such as penis, lens of eyes, fascia (part of connective tissue), etc., organs/tissues that classic mathematical phantoms did not include because they were not considered for the study of stochastic effects, has been revealed. Absorbed doses due to photons, obtained following the same simulation methodology, are larger than those due to neutrons, reaching values 100 times larger as the primary beam is approached. However, for organs far from the treated volume, absorbed photon doses can be up to three times smaller than neutron ones. Calculations using voxel phantoms permitted to know the organ dose conversion coefficients per MU due to secondary neutrons in the complete anatomy of a patient.