Purpose:It is the goal of this study to use both Monte Carlo (MC) simulation and the pencil beam dose algorithm (PBA) in the treatment planning system to investigate Patient scatter factor (PSF) and Compensator scatter factor (CSF) for calibrating the dose per monitor unit (DMU) for a passive scattering proton therapy system.Materials and Methods: PSFs and CSFs for brain, lung, pancreas, and prostate treatment sites were calculated by using MC simulation and PBA from the treatment planning software to evaluate the agreement between the two.Results:This study shows that the CSF values are always greater than 1, with some reaching nearly 4% above unity, and depending strongly on the shape of the compensator. Monte Carlo and PBA-calculated CSF factors agree very well, with average differences below 1%. PSF values calculated in this study ranged from 0.919 to 1.023 and are largely dependent on the type of tissue heterogeneities in the treatment field. Monte Carlo and PBA-calculated PSF factors show differences, with the largest discrepancies seen in lung cases, with an average difference of 1.9%. It is also shown that dense bone will drive a PSF to values greater than unity, while large quantities of air decrease the PSF to below unity.Conclusion:We have showed that the compensator and patient anatomy can have a significant impact on clinical proton dose distribution. It is recommended that both Monte Carlo and treatment planning system should be used to take these factors into account in the final DMU calculation.