To predict the risks of late, radiation-induced effects for young patients with Hodgkin's lymphoma (HL), non-Hodgkin's lymphoma (NHL), or breast cancer (BC) if treated with intensity modulated proton therapy (IMPT) compared to 3D conformal photon radiotherapy (3D-CRT). Late effects considered were cardiac mortality and secondary cancer in the lungs and breasts (for female patients). Patient data were acquired for twenty-six patients (ages 12-29) who were treated with 3D-CRT for HL, NHL, or BC in 2010. Original CT simulation images were used to re-plan the patients with IMPT using commercially-available treatment planning software. The contours of the organs at risk were reviewed by a single physician and modified for consistency. The dose-volume data of the 3D-CRT plans and the new IMPT plans were analyzed to model the risks of late effects. The relative seriality model was used to predict excess risk of cardiac mortality at fifteen years post-irradiation. A modified linear quadratic model was used to predict the Excess Absolute Risk (EAR) for induction of lung cancer and breast cancer at thirty years post-irradiation. For 3D-CRT and IMPT respectively, the mean excess risks of cardiac mortality were 0.9% and 0.5%. Mean EARs for lung cancer were 17.5 cases per 10,000 persons per year (PY) and 10.1 PY. Mean EARs for breast cancer were 8.2 PY and 2.8 PY. IMPT may significantly reduce the risks of radiation-induced cardiac mortality and secondary cancer in the lungs and breasts of young patients receiving radiotherapy for HL, NHL, or breast cancer.