This study aimed to evaluate the absorbed doses received by the organs at risk (OARs) following prostate treatment with permanent Iodine-125 (125I) brachytherapy seeds. In order to simulate an enlarged abnormal prostate due to malignancy, the MIRD5 adult male anthropomorphic phantom (readily available in the Geant4 Monte Carlo package) was modified by increasing the prostate volume to 35 cm3. The permanent seeds were constructed with an outer cylindrical dimension of 4.5 mm (length) × 0.8 mm (diameter). The effects of various activity per seed (0.5, 0.6 and 0.8 mCi), number of seeds (62, 78, 94 and 110 seeds) and radionuclides, i.e. Palladium-103 (103Pd), 125I and Cesium-131 (131Cs), towards the absorbed dose to the OARs (i.e. rectum, urinary bladder and both testicles) were investigated. In this study, prostate dose of up to 237 Gy was simulated, which resulted in 11 Gy dose to rectum, 7 Gy to urinary bladder and 4 Gy to each testicle. The doses were considered as reasonable, given the low dose rate nature of the treatment, allowing tissue repair for the OARs. Optimal seeds arrangement was found to consist of 78 or fewer seeds, as it resulted in the lowest dose to the OARs. For similar prostate dose, 103Pd resulted in the lowest dose to the OARs, followed by 125I and 131Cs. Permanent seed brachytherapy allows high dose to be delivered to the prostate, while ensuring minimal dose to the OARs.