Northern Saw-whet Owls (Aegolius acadicus) breed throughout the boreal forest of North America, but little is known about their population trends or distribution within this region. Analysis of stable hydrogen isotopes (δ²H) in feathers can delineate origins of a variety of avian migrants, but raptors are reported to have high intra-feather isotopic variance and mean δ²H values higher than predicted from δ²H isoscapes specific to raptor feathers, making assignment of geographic origin sometimes difficult. We examined the applicability of δ²H analysis of saw-whet owl feathers to delineating origins of migrants and to assessing differences in the migratory behavior of adult and young owls by using multiple generations of feathers from owls captured during fall migration at the Delta Marsh Bird Observatory, Manitoba, 2006–2007. Values of δ²H in saw-whet owl feathers were higher than predicted from a δ²H isoscape specific to raptor feathers and from patterns of movements inferred from analysis of band recoveries. This effect was pronounced in adults, while values of δ²H in feathers of hatching-year owls fell primarily within the range predicted for the boreal forest northwest of Delta Marsh. Significant differences in δ²H values among feather generations suggest that physiological or behavioral differences between adults and young give rise to greater ²H enrichment in adult feathers. These results indicate that current δ²H isoscapes for feathers cannot be used to track adult saw-whet owls reliably and further research into the mechanisms of ²H enrichment in owl feathers is required.