Inverse planning and intensity modulated (IM) X-ray beam treatment techniques can achieve significant improvements in dose distributions comparable to those obtained with forward planned proton beams. However, intensity modulation can also be applied to proton beams and further optimization in dose distribution can reasonably be expected. A comparative planning exercise between IM X-rays and IM proton beams was carried out on two different tumor cases: a pediatric rhabdomyosarcoma and a prostate cancer. Both IM X-rays and IM protons achieved equally homogenous coverage of the target volume in the two tumor sites. Predicted NTCPs were equally low for both treatment techniques. Nevertheless, a reduced low-to-medium dose to the organs at risk and a lesser integral non-target mean dose for IM protons in the two cases favored the use of IM proton beams.