We used tissue printing and specific immunostaining to examine the localization of the alternative oxidase (AOX) protein in correlation with measurements of AOX capacity. Selected root and hypocotyl regions were analyzed during the first 14 d of growth. It is shown that AOX protein is localized in the apical meristem and in developing xylem. The temporal pattern of expression is coincident with the evolution of AOX capacity. Data suggest that AOX expression is linked to xylem differentiation. Since heat is a major product of the alternative pathway, we speculate that thermogenesis is implicated in morphogenesis.