The issues of whether, where, and to what extent carbon isotopic fractionations occur during respiration affect interpretations of plant functions that are important to many disciplines across the natural sciences. Studies of carbon isotopic fractionation during dark respiration in C-3 plants have repeatedly shown respired CO2 to be C-13 enriched relative to its bulk leaf sources and C-13 depleted relative to its bulk root sources. Furthermore, two studies showed respired CO2 to become progressively C-13 enriched during leaf ontogeny and C-13 depleted during root ontogeny in C-3 legumes. As such data on C-4 plants are scarce and contradictory, we investigated apparent respiratory fractionations of carbon and their possible causes in different organs of maize plants during early ontogeny. As in the C-3 plants, leaf-respired CO2 was C-13 enriched whereas root-respired CO2 was C-13 depleted relative to their putative sources. In contrast to the findings for C-3 plants, however, not only root- but also leaf-respired CO2 became more C-13 depleted during ontogeny. Leaf-respired CO2 was highly C-13 enriched just after light-dark transition but the enrichment rapidly decreased over time in darkness. We conclude that (i) although carbon isotopic fractionations in C-4 maize and leguminous C-3 crop roots are similar, increasing phosphoenolpyruvate-carboxylase activity during maize ontogeny could have produced the contrast between the progressive C-13 depletion of maize leaf-respired CO2 and C-13 enrichment of C-3 leaf-respired CO2 over time, and (ii) in both maize and C-3 leaves, highly C-13 enriched leaf-respired CO2 at light-to-dark transition and its rapid decrease during darkness, together with the observed decrease in leaf malate content, may be the result of a transient effect of light-enhanced dark respiration.