Monitor the milk thistle plant in the mid to late summer. You should not try to harvest the seeds until the seed head is brown. When the seed head is brown, the seeds will have the highest medicinal quality.
Put on gardening gloves.
Cut seed heads with kitchen shears. Store the seed heads in a basket until you remove as many seed heads as you want from the milk thistle plants.
Remove the seeds from the pods and set them aside on a separate tray. If any leaves, pods, hairs or other debris get onto the tray, simply remove them and throw them away. You can use the seeds at this point, when they are fresh. If you want dry seeds, proceed to Step 5.
Dry the seeds uncovered on the tray in a window in the sun for two days.
Store the seeds in a glass jar with a tight lid in a cool, dry place, such as the refrigerator or pantry.