Protons and heavy ion particles are considered to be ideal particles for use in external beam radiotherapy due to superior properties of the dose distribution that results when these particles are incident externally and due to their relative biological effectiveness. While significant research has been performed into the properties and physical dose characteristics of heavy ions, the nuclear reactions (direct and fragmentation) undergone by He4, C12 and Ne20 nuclei used in radiotherapy in materials other than water is still largely unexplored. In the current project, input code was developed for the Monte Carlo toolkit Geant 4 version 9.3 to simulate the transport of several mono-energetic heavy ions through water. The relative dose contributions from secondary particles and nuclear fragments originating from the primary particles were investigated for each ion in both water and dense bone (ICRU) media. The results indicated that the relative contribution to the total physical dose from nuclear fragments increased with both increasing particle mass and with increasing medium density. In the case of 150 MeV protons, secondary particles were shown to contribute less than 0.5% of the peak dose and as high as 25% when using 10570 MeV neon ions in bone. When water was substituted for a bone medium, the contributions from fragments increased by more than 6% for C12 and Ne20.