The part of the stem of an embryo, or young seedling, below the cotyledons.

As the plant embryo grows at germination, it sends out a shoot called a radicle that becomes the primary root and penetrates down into the soil. After emergence of the radicle, the hypocotyl emerges and lifts the growing tip (usually including the seed coat) above the ground, bearing the embryonc leaves (called cotyledons) and the plumule that gives rise to the first true leaves.

The hypocotyle is the primary organ of extension of the young plant and develops into the stem.