Saving tomato seeds is not difficult, but you need to use open-pollinated varieties (as most heirloom tomatoes are) in order to have them grow true to type.
1. Start by taking the best tomatoes from a number of plants of that variety will give you a good genetic mix. They needn't be rotten, just ripe.
2. Cut the fruits in half at their waistlines, and squeeze their seeds into a labeled container such as a glass jar.
3. Add several inches of water to the jar and set it aside, out of direct sunlight but in a warm spot. A flotilla of fungal matter will form after a few days, but you may cover the jar to avoid the smell, deter fruit flies and prevent a tidy family member from throwing out the whole thing. Keep the lid loose, though, to encourage the fermentation that is the key to this little operation. The gel coating that has kept the seeds from germinating will break down, and any good, viable seeds will sink to the bottom. Stir from time to time.
4. After no more than five days, spoon off and discard the moldy debris on the surface, and pour off the water. Add fresh water to the seeds, stir and let them settle again. Do this until the seeds are clean, then drain them well in a fine strainer and spread them on a screen or a plate so that they'll dry quickly, out of the sun.
5. When they are absolutely dry and are easily separated with your fingers, they can be stored in an airtight jar or plastic bag and will keep for at least five years.
Source: Barbara Damrosch http://kitchengardeners.org/questions/how-do-i-save-tomato-seeds
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