When tomato seedlings are three or four inches tall and have their second pair of leaves, it's time to take them out of their crowded containers and put them into deeper, roomier ones. (If you started seedlings in individual containers at least three inches square, simply thin out the weaker plants by snipping them off at the soil line and leaving the strongest one.)
Choosing The Right Container
Any part of the tomato stem that's covered with soil will develop roots, and a large root system is important for transplants. Try using a deeper container and set the plants lower than they were growing before - right up to the lowest set of leaves, if you can. Use the same soil mix that you used to start your seeds. Here are some hints for successful repotting:
Water the tomatoes well before you start to repot. Moist soil will cling to the roots and protect them from drying.
Lever the seedlings out of the soil with a small utensil, such as a table knife. Lift the plants by their leaves, if necessary, rather than by their stems - if you lose a leaf, it can grow back, but if you break the stem below the leaves, the plant won't make it.
Set the seedlings about three inches apart in their new container(s). Firm the soil around them, and water gently. Keep out of bright sunlight for a day or two.
Fertilize once a week with liquid fertilizer. Follow the directions for dilution on the label. Some recommend different dilution and application rates for seedlings versus houseplants or full-grown plants.
The Second Transplant
Before the tomato plants can be transplanted successfully to the garden, they need to develop strong root and top growth. To be sure their seedlings have a good root system, many gardeners prefer to repot them a second time before setting them out in the garden. Wait until seedlings are six to 10 inches tall. A good rule is to transplant when the height of your seedling is three times the diameter of its pot. Pot them up individually in half-gallon milk cartons or four- to six-inch-diameter pots. Again, you can plant them right up to their first set of leaves.
If your seedlings are getting tall and spindly, the room temperature may bee too high, the light too weak, or you're using too much fertilizer (or a combination of all three). Review seedling needs in Starting Tomatoes from Seed and adjust growing conditions as needed. Transplanting leggy seedlings deeply helps them to root along their stems, thus reducing the problem, but the best solution is to give your young plants proper growing conditions in the first place.