A key role in the treatment of cancer is to kill the tumor cells while at the same time minimizing the amount of damage to the surrounding normal tissue.Accurate knowledge of the physical and biological properties of the particles used in radiation therapy, such as light ions, is therefore needed.Calculation of the nuclear reactions of the primary and secondary particles with matter can be performed with either semi-inclusive or exclusive models.To make a correct treatment planning for radiation therapy, the transport of all primary and secondary particles must also be simulated.The transport of particles, such as light and heavy ions can be performed with deterministic or stochastic, Monte Carlo, codes.In this paper, we compare calculated total depth-dose distributions, attenuation of primary particles, and fluence distributions of secondary particles from the reactions of 200, 300 and 400 MeV/nucleon Li, B and C in water using the well known one dimensional deterministic particle and heavy ion code Heavy Ion BRAgg curve Calculator (HIBRAC), which has been used since 1994 for heavy ion therapy, with analytical expressions, and simulations using the three dimensional Monte Carlo Particle and Heavy Ion Transport code System (PHITS).These calculations are compared with results from the transport model used in the treatment planning system for the heavy ion treatment at the Institute of Modem Physics (IMP) in Lanzhou, China.Experiences from treatment of deep seated tumors at IMP will also be presented.Advantages and disadvantages with semi-inclusive and exclusive models, as well as with one dimensional deterministic and three dimensional stochastic codes are discussed.