Fill a container with moist paper towels or peat moss. Spread the apple seeds across the towels or moss.
Seal the container and put it in the refrigerator at 35 to 40 degrees Fahrenheit. Leave the container in the refrigerator for about 60 days. During this time, the apple seeds may germinate.
Remove the container after 60 days, whether or not the seeds have germinated. Prepare one 3-inch container per apple seed. Add enough soil to fill each container.
Bury each apple seed under 1 inch of soil. Cover the containers with plastic to raise humidity. Poke a few holes in the plastic.
Put the apple seeds in a warm place out of direct sunlight. Ensure the soil stays moist. Apple seed germination occurs in a few days or a few months.