Purpose: To evaluate three-dimensional (3D) ultrashort echo time (UTE) MRI regarding image quality and suitability for functional image analysis using gradient-echo sequences in breath-hold and with self-navigation. Materials and Methods: In this prospective exploratory study, 10 patients (mean age, 21 years; age range, 558 years; five men) and 10 healthy control participants (mean age, 25 years; age range, 1039 years; five men) underwent 3D UTE MRI at 3.0 T. Imaging was performed with a prototypical stack-of-spirals 3D UTE sequence during single breath holds (echo time [TE], 0.05 msec) and with a self-navigated Koosh ball 3D UTE sequence at free breathing (TE, 0.03 msec). Image quality was rated on a four-point Likert scale. Edge sharpness was calculated. After semiautomated segmentation, fractional ventilation was calculated from MRI signal intensity (FVSI) and volume change (FVVol). The air volume fraction (AVF) was estimated from relative signal intensity (aortic blood signal intensity was used as a reference). Means were compared between techniques and participants. The Wilcoxon signed rank test and Spearman rank correlation were used for statistical analyses. Results: Image quality ratings were equal for both techniques. However, stack-of-spirals breath-hold UTE was more susceptible to motion and aliasing artifacts. Mean FVSI was higher during breath hold than at free breathing (mean +/- standard deviation in milliliters of gas per milliliters of parenchyma, 0.17 mL/mL +/- 0.06 [minimum, 0.07; maximum, 0.34] vs 0.11 mL/mL +/- 0.03 [minimum, 0.06; maximum, 0.17], P = .016). Mean FVSI and FVVol were in good agreement (mean difference: at breath hold, -0.008 [95% confidence interval {CI}: 0.007, -0.024]; rho = 0.97 vs free breathing, -0.004 [95% CI: 0.007, -0.016]; rho = 0.91). AVF correlated between both techniques (rho = 0.94). Conclusion: Breath-hold and self-navigated 3D UTE sequences yield proton densityweighted images of the lungs that are similar in quality, and both techniques are suitable for functional image analysis. Summary Three-dimensional ultrashort echo time gradient-echo sequences are promising tools for acquisition of proton density-weighted lung MR images within a single breath hold or at free breathing, providing high spatial resolution and allowing for functional image analysis such as ventilation or air volume fraction.