In south-eastern Australia, surface-retained wheat stubble can reduce the growth and yield of canola as a result of reductions to the quality and quantity of light under the stubble and the associated elongation of the hypocotyl. This paper reports a series of pot experiments that examined the effect of hypocotyl elongation on the leaf area development of canola, the allocation of dry mass, and the absolute and relative growth rates compared to non-etiolated seedlings. The primary aim was to determine the magnitude of the growth reductions caused by hypocotyl elongation in canola seedlings under controlled conditions. Seedling hypocotyl elongation was induced by growing canola seedlings in narrow poly-pipe tubing of different lengths placed over the seedlings as they began to emerge through the soil, and removing the shade cloth covering the top of the tube when the cotyledons had reached it, to mimic the plant reaching and overtopping a stubble layer. Plants with longer hypocotyls had smaller root systems, less leaf area and less leaf and root biomass. These plants had lower relative growth rates than plants that allocated fewer resources to hypocotyls and more to roots and leaves. The magnitude of the growth responses observed in these experiments was similar to those of plants with long hypocotyls growing through stubble layers in previously reported field studies. This suggests that a significant portion of the effect of stubble observed in the field under stubble retention is due to the re-allocation of resources to the production and growth of the hypocotyls, rather than other biochemical effects of the stubble.