To investigate the feasibility of lung ventilation-based treatment planning, computed tomography and hyperpolarized (HP) helium-3 (He-3) magnetic resonance imaging (MRI) ventilation images of 6 subjects were coregistered for intensity-modulated radiation therapy planning in Tomotherapy. Highly-functional lungs (HFL) and less-functional lungs (LFL) were contoured based on their ventilation image intensities, and a cylindrical planning-target-volume was simulated at locations adjacent to both HFL and LFL. Annals of an anatomy-based plan (Plan 1) and a ventilation-based plan (Plan 2) were generated. The following dosimetric parameters were determined and compared between the 2 plans: percentage of total/HFL volume receiving ≥20 Gy, 15 Gy, 10 Gy, and 5 Gy (TLV 20, HFLV 20, TLV 15, HFLV 15, TLV 10, HFLV 10, TLV 5, HFLV 5), mean total/HFL dose (MTLD/HFLD), maximum doses to all organs at risk (OARs), and target dose conformality. Compared with Plan 1, Plan 2 reduced mean HFLD (mean reduction, 0.8 Gy), MTLD (mean reduction, 0.6 Gy), HFLV 20 (mean reduction, 1.9%), TLV 20 (mean reduction, 1.5%), TLV 15 (mean reduction, 1.7%), and TLV 10 (mean reduction, 2.1%). P-values of the above comparisons are less than 0.05 using the Wilcoxon signed rank test. For HFLV 15, HFLV 10, TLV 5, and HTLV 5, Plan 2 resulted in lower values than plan 1 but the differences are not significant ( P-value range, 0.063–0.219). Plan 2 did not significantly change maximum doses to OARs ( P-value range, 0.063–0.563) and target conformality ( P = 1.000). HP He-3 MRI of patients with lung disease shows a highly heterogeneous ventilation capacity that can be utilized for functional treatment planning. Moderate but statistically significant improvements in sparing functional lungs were achieved using helical tomotherapy plans.