Tomatoes rot on the vine for several reasons, including inconsistent moisture, too much sun, pest infestation and exposure to disease. The first three problems can be addressed as the plant grows to reduce rot on future fruit, but crops that are exposed to disease should be destroyed.
Pest infestation is one of the easiest problems to diagnose because the bugs are often present and their effects are distinct. Stink bugs create dark spots on tomatoes when they feed, leaving an area that turns yellow or stays green when the fruit ripens. Hornworns are often found under the leaves, and their feeding marks are apparent on leaves and fruit.
When tomatoes receive too much sun, a condition called sunscald occurs and the fruits develop white patches with a leathery texture. Blossom end rot occurs when tomatoes receive inconsistent moisture, inhibiting the plant's ability to receive calcium. The rot causes light brown spots on the end of the tomato, and these spots eventually turn black.
Tomatoes are susceptible to blight, tobacco mosaic virus and wilt. Signs of these diseases include gray, moldy areas on the fruit, as well as distorted leaves and cankers on the fruit or the stem. Diseases that affect tomatoes can remain in the soil, and the Colorado State University extension service recommends planting other crops in affected areas for at least two years after the disease is discovered.