Wait until they're ready. Most grains, nuts and beans are ready for harvest three to five days after germination. Greens, such as alfalfa, radish, wheatgrass, are ready in one to two weeks. Most sprouts are ready to consume just after they develop their first two leaves and lose their yellow color.
Harvest ripe sprouts by gripping them near their tops and wiggling them free of the planting tray, roots and all. Keep your other hand firmly on the tray to keep it from lifting off the table. It's rare for all sprouts to ripen at the same time. Leave immature sprouts for later.
Place the sprouts in a colander and rinse them under running water. If necessary, remove the seed hulls stuck to the sprouts' leaves. Often, a stiff spray of water removes the seed hull.
Cut the roots off plants that grew in soil.