This is probably blossom end rot. It occurs at the bottom of the tomato and sort of looks like a bruise that may or may not be indented somewhat. Crushed egg shells in the dirt will replace a calcium shortage which is frequently the cause. Also, too much water and/or fertilizer (indicated particularly if you have plants that are very tall but not bearing much fruit) can cause blossom end rot. Pick the affected fruit as soon as you notice the problem so the plant's energy is spent on healthy fruit instead. Usually only affects some of the fruit on a plant, and most often only the first fruits.

Hardiness Zone: 6a
Debi from Niagara Falls, NY
Calcium in the soil is dissolved by water and taken up by the plant's roots. In conditions of high moisture stress (lots of rain or overwatering), this water is taken up by the plant's vascular tissue very quickly and the water moves more rapidly than usual from the plant's roots to its leaves. A plant loses most of its water through the leaves (transpiration), so naturally after a large uptake of water, most of the calcium is left behind (deposited) in the leaves, before it has the chance to be evenly distributed throughout the entire plant (especially to the fruits, which are the last to receive it anyway). When most of the calcium is deposited in the leaves, it causes a localized deficiency of calcium in the fruit. This eventually causes the cells to collapse, producing the symptoms of blossom-end rot. Blossom-end rot can also occur in plants experiencing rapid leaf growth due to over-fertilization (especially with nitrogen), because the larger leaves increase the amount of surface area available for transpiration to occur, throwing the plant's systems off balance.
To prevent blossom-end rot, here are some things you can do:
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By LI Roe
By Lynda
I'm growing tomatoes in a Topsy Turvy planter. The fruit is about 1.5 inches across, and the bottom is discolored (beige). What is the cause, and what can I do to save the other (green) tomatoes?
Hardiness Zone: 9b
By sandralee406 from Beaumont, TX
I have a Topsy Turvy tomato planter and my tomatoes are turning dark brown or black on the bottom. I used miracle grow moisture control for the whole plant. Does anyone have clues or ideas for me? My plant is starting to look wilted.
Hardiness Zone: 8b
By Chris from Round Rock, TX
Topsy Turvy is a fun way to grow tomatoes, isn't it? Who would ever have thought? We'd plant flowers (something like petunias or nasturtiums) in the top part of our bucket, which often would cascade or drape over the edge. Made it look so pretty. We made our own Topsy Turvy containers using 5 gal wallpaper paste plastic buckets. Worked just great! Good luck to you.
Julia in Boca Raton, FL (05/11/2010)
By PookaRina
By suegordon123
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