Hypocotyl is a botanical term for a part of a germinating seedling of a seed plant. 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.

The early development of a monocot seedling like corn and other grasses is somewhat different. A structure called the coleoptile, essentially a part of the cotyledon, protects the young stem and plumule as growth pushes them up through the soil. A mesocotyl — that part of the young plant that lies between the seed (which remains buried) and the plumule — extends the shoot up to the soil surface, where secondary roots develop from just beneath the plumule. The primary root from the radicle may then fail to develop further. The mesocotyl is considered to be partly hypocotyl and partly cotyledon (see scutellum).

Not all monocots develop like the grasses. The onion develops in a manner similar to the first sequence described above, the seed coat and endosperm (stored food reserve) pulled upwards as the cotyledon extends. Later, the first true leaf grows from the node between the radicle and the sheath-like cotyledon, breaking through the cotyledon to grow past it.

In some plants, the hypocotyl becomes enlarged as a storage organ. Examples include cyclamen and gloxinia .