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.