Most tomato fruit problems are disorders, not diseases: black sunken bottoms are blossom-end rot, cracks come from uneven water, scarred misshapen fruit is catfacing, and cloudy spots are stink bug feeding. Pick what you see below to identify the problem, learn whether the fruit is safe to eat, and fix the cause.
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What Your Result Means: the tool names the most likely problem, whether it is a disorder, insect, or disease, what causes it, what to do, and whether the fruit is safe to eat. Disorders are fixed by care such as watering, not sprays. Never eat visibly rotten or moldy fruit.
What Is Wrong With My Tomato Fruit?
Look at where the damage is (bottom, top, or side), what it looks like (sunken, cracked, spotted, or holed), and whether it is dry or rotting. Dry, cosmetic damage is usually a disorder or insect; soft, spreading rot points to disease.
- Look closely at the damaged fruit, and at the leaves too.
- Pick the closest match from the list.
- Read the cause and fix, and whether the fruit is safe to eat.
- Follow the next-step tool for prevention.
Tomato Fruit Problems at a Glance
| What You See | Likely Problem | Type |
|---|---|---|
| Dark, sunken, leathery patch on the bottom | Blossom-End Rot | Disorder |
| Cracks radiating from the stem or in rings around it | Fruit Cracking | Disorder |
| Misshapen with deep crevices and scars at the bottom | Catfacing | Disorder |
| Thin brown scar like a zipper from stem to bottom | Zippering | Disorder |
| Pale, white, or blistered patch on the side facing the sun | Sunscald | Disorder |
| Cloudy white or yellow spots just under the skin | Stink Bug Damage (Cloudy Spot) | Insect |
| Yellow or green shoulders, or blotchy uneven ripening | Uneven Ripening (Yellow Shoulder) | Disorder |
| Sunken round spots with dark centers on ripe fruit | Anthracnose | Fungal disease |
| Greasy, olive-green to brown-black patches, often near the top | Late Blight | Water mold (acts fast) |
| Dark, leathery, sunken patch at the stem end, sometimes with rings | Early Blight on Fruit | Fungal disease |
| Tiny dark specks or small raised, scabby spots | Bacterial Speck or Spot | Bacterial disease |
| Round holes or tunnels into the fruit | Caterpillar Damage (Fruitworms or Hornworms) | Insect |
How Does the Fruit Problem Identifier Work?
It matches the symptom you choose to the cause University of Maryland Extension and Clemson Extension describe for it, and adds a first response and an eating-safety note.
Cause -> type: disorder, insect, or disease
Disorders -> fix watering, temperature, or feeding
Diseases -> remove affected fruit and plants, keep foliage dry
Rot or mold -> do not eat
Worked Example
Say your first tomatoes are lumpy, with deep scars and holes at the bottom, after a cold spell in late spring. The match is catfacing, caused by flowers forming in temperatures below about 50°F. There is nothing to treat; the fruit is safe once the scars are cut out, and fruit set in warmer weather will be normal. Next year, check the soil temperature and wait for warmer nights before planting out.
How to Prevent Tomato Fruit Problems
- Water deeply and evenly and mulch, to prevent blossom-end rot and cracking.
- Do not overfeed nitrogen, which is linked to both.
- Plant out once it is warm, to avoid catfacing.
- Keep leaf cover to shade fruit and prevent sunscald.
- Pick at first color before storms and heavy pest pressure.
- Keep leaves dry and rotate beds to limit fruit rots.
Accuracy and Limitations
This is a guide to the most likely cause, not a lab diagnosis.
What It Does Well: separates harmless disorders from diseases and insects and says whether fruit is safe to eat.
What It Does Not Do: confirm a disease. Several problems can appear together, and rots can follow cracks or insect damage. For a sure answer, take a sample to your local extension office. This is general guidance, not professional advice.
Methodology
Method: a symptom-to-cause lookup for 12 common tomato fruit problems. Descriptions and causes: catfacing below 50°F, zippering, cracking, blossom-end rot, sunscald, stink bug cloudy spot, anthracnose, late blight, early blight, and bacterial speck and spot (University of Maryland Extension, Key to Common Problems of Tomatoes; Clemson Home and Garden Information Center). Uneven ripening: heat over about 90°F or potassium imbalance, matching our Plant Problem Diagnosis tool. Caterpillars: handpicking and Bt, matching our Plant Problem Diagnosis tool. Eating safety: cut away damaged parts; never eat rotten or moldy fruit. No dosing.
Sources: University of Maryland Extension – Key to Common Problems of Tomatoes, Clemson HGIC – Tomato Diseases and Disorders. Last reviewed: September 28, 2026 · Reviewed by Aiza Anwar.
Frequently Asked Questions
What causes black bottoms on tomatoes?
Blossom-end rot, a disorder caused by calcium not reaching the fruit, usually because of uneven watering. Water deeply and evenly and mulch; the rest of the fruit is safe once the bad part is cut away.
Why are my tomatoes cracking?
Swings in soil moisture, long rainy spells, heavy dews, or too much nitrogen make fruit swell faster than the skin can stretch. Even watering and mulch help.
What causes misshapen tomatoes with scars on the bottom?
Catfacing, which University of Maryland Extension links to temperatures below 50°F around transplanting. Later fruit is usually normal.
What are the white cloudy spots under tomato skin?
Usually stink bug feeding, called cloudy spot. The spots are corky but harmless; cut them out and eat the rest.
Why do my tomatoes have yellow shoulders?
Often heat above about 90°F on exposed fruit or a potassium imbalance. Light shade and balanced feeding help.
Can I eat tomatoes with blossom-end rot or cracks?
Yes, if you cut away the damaged part and there is no mold or rot. Never eat visibly rotten or moldy fruit.
What does late blight look like on tomato fruit?
Greasy, olive-green to dark brown patches, often on the upper part of the fruit, which can turn into a wet rot. It spreads fast in cool, wet weather.
What is the brown zipper line on my tomato?
Zippering, a harmless scar from flower parts sticking to the young fruit, often in cool weather.
What makes holes in tomatoes?
Caterpillars such as tomato fruitworms and hornworms. Handpick them and check under leaves; Bt controls young caterpillars.
Related Tomato Tools
See the Full Problems & Solutions Guide
This tool gives general guidance on the likely cause of tomato fruit problems, not a diagnosis or professional advice. Never eat visibly rotten or moldy fruit. Spotted an error? Tell us here.