Holes in My Tomatoes: Which Pest Is Ruining the Fruit?

Holes in tomatoes are most often the work of tomato fruitworms (one clean round entry hole), hornworms (large shallow gouges), birds (peck marks in ripe fruit), slugs (rasped pits where fruit touches soil), or squirrels (single bites, fruit carried off). Sunken leathery patches on the bottom of the fruit aren't a pest at all — that's blossom-end rot.

Most likely causes

  • Tomato fruitworm — one clean round hole near the stem, tunneled interior
  • Hornworm — big shallow ragged gouges in the fruit surface, heavy leaf loss nearby
  • Birds — triangular peck marks in the ripest, reddest fruit
  • Slugs — shallow rasped pits on fruit resting on or near the soil
  • Squirrels or chipmunks — one big bite taken, or half-eaten fruit left on a fence
  • Blossom-end rot — dark sunken patch on the bottom; a nutrient problem, not a pest

Compare the possible causes

Possible cause Key signs When it happens How likely
Tomato fruitworm A single clean round hole, often near the stem end, leading to a tunneled, messy interior Midsummer through harvest, worst in warm regions Very common
Hornworms Large shallow ragged gouges chewed into the fruit surface, paired with stripped leaves and bare stems above Midsummer to early fall Common
Birds Triangular or slash-shaped peck marks, almost always in the ripest fruit highest on the plant Hot, dry spells in summer, when birds are seeking moisture Common
Slugs and snails Shallow rasped pits and irregular holes on fruit touching the ground or mulch, with slime trails nearby Damp weather and cool nights; damage appears overnight Common
Squirrels and chipmunks One large bite out of a fruit, whole tomatoes missing, or half-eaten fruit abandoned on a fence rail or patio Daytime, often mid to late summer during dry spells Common
Blossom-end rot (not a pest) A dark, sunken, leathery patch on the blossom end (bottom) of the fruit — no hole, no tunnel, no droppings Early in the harvest season, especially after uneven watering Very common

Visual clues to check

  • Look at the hole shape: one clean round bore hole means fruitworm; a wide shallow gouge means hornworm; a triangular stab means birds
  • Check where the damaged fruit sits: soil-contact damage low on the plant points to slugs; damage on the highest, ripest fruit points to birds
  • Search for moved fruit: tomatoes with a single bite found feet away from the plant mean squirrels or chipmunks
  • Cut a suspect fruit open: internal tunnels and droppings confirm fruitworm
  • Inspect the bottom of the fruit: a symmetrical sunken leathery patch with no opening is blossom-end rot, not an animal
  • Check the foliage: heavy leaf loss alongside gouged fruit means a hornworm is still on the plant
  • Look for slime trails on mulch and lower stems in the morning after damp nights

The causes in detail

Tomato fruitworm

The tomato fruitworm — the same caterpillar known as the corn earworm — bores into green or ripening fruit and feeds inside, leaving a watery cavity filled with droppings. One caterpillar can move on and damage several fruits. From the outside the entry hole can look small and tidy, which is why the rot inside surprises people; cut a suspect fruit open before assuming it's salvageable.

Hornworms

Hornworms prefer foliage, but big ones gouge fruit too — wide, superficial scars rather than neat entry holes. If your tomatoes have surface craters and the plant is also missing leaves, hunt for the caterpillar: check within a foot of the freshest damage and look for barrel-shaped black droppings on the leaves below. At 3 to 4 inches long they're the giants of the tomato patch, yet their camouflage is excellent.

Birds

Mockingbirds, robins, and other backyard birds peck ripe tomatoes mostly for the water inside, which is why damage spikes during drought. They target the reddest fruit and rarely finish one before sampling another. A birdbath kept full nearby genuinely reduces damage, and picking fruit at the 'breaker' stage — just blushing — lets it ripen safely indoors with no loss of flavor.

Slugs and snails

Slugs can't climb far up a tomato plant, so their damage is concentrated on low-hanging fruit that rests on soil or wet mulch. The wounds look scraped rather than bitten, often enlarging into a cavity as the fruit softens. Keeping fruit off the ground — with cages, stakes, or a dry buffer of gravel — removes most of the risk.

Squirrels and chipmunks

Squirrels are the classic 'one bite and gone' offender: they pluck a ripening tomato, taste it, drop it, and take another the next day. Like birds, they're often after moisture as much as food. Finding fruit carried several feet from the plant — on a fence, deck rail, or lawn — is the strongest evidence, since insects and slugs eat in place.

Blossom-end rot (not a pest)

Blossom-end rot is routinely mistaken for pest damage, but nothing ate the fruit — it's a calcium delivery problem inside the plant, almost always triggered by inconsistent watering. The patch is symmetrical, dry, and always on the bottom of the fruit. Fix it going forward with deep, even watering and mulch; affected fruit won't recover, but the next flush usually grows in clean.

When to worry

  • Multiple fruits with bore holes each week — fruitworms move from fruit to fruit and losses add up fast
  • Damage appearing daily in daylight hours, which suggests squirrels or birds working the plant on a routine
  • Nearly every low fruit pitted after rain — a large slug population living in the mulch
  • Most of the crop showing sunken bottoms — a watering schedule problem worth fixing before the next flush of fruit

What to do now

  1. Pick off and destroy any fruit with bore holes — leaving it on the vine feeds the caterpillar and invites rot
  2. Handpick hornworms after tracing droppings upward from the leaves below
  3. Harvest fruit at the breaker stage (first blush of color) and ripen it on a counter, out of reach of birds and squirrels
  4. Stake or cage plants so no fruit touches soil or mulch, and trap slugs under a board you flip each morning
  5. Put a filled birdbath or shallow water dish near the garden in dry spells — much bird and squirrel damage is really thirst
  6. Drape bird netting over cages, secured at the bottom so animals can't slip underneath
  7. Keep watering deep and consistent, and mulch the bed to prevent blossom-end rot on later fruit

What not to do

  • Don't eat the undamaged-looking part of fruit that animals have bitten — wildlife bites and droppings can contaminate the flesh; compost it instead
  • Don't spray insecticide onto ripening fruit hoping to stop squirrels or birds — it doesn't work on them and makes the harvest unsafe
  • Don't treat blossom-end rot with pest control products; nothing is eating the fruit and no spray will fix a watering problem
  • Don't leave bitten or fallen fruit lying in the garden — it trains squirrels, raccoons, and slugs to keep coming back
  • Don't drape netting loosely over plants; birds and snakes can tangle in slack netting, so pull it taut over a frame or cage

Think you know the suspect?

These animals commonly cause this clue — see their full sign profiles:

Frequently asked questions

What makes a perfectly round hole in a tomato?

A single clean round hole — usually near the stem — is the classic sign of a tomato fruitworm that bored in to feed. Cut the fruit open and you'll typically find tunnels and droppings inside. Remove and destroy the fruit, then check neighboring tomatoes, since one caterpillar damages several.

Are tomatoes with holes still safe to eat?

It depends on the cause. Insect-damaged fruit is safe if you cut well around the tunnel and the rest is firm and smells normal, and blossom-end rot fruit is fine once the leathery patch is removed. Fruit bitten by birds or mammals should be discarded because of contamination risk.

How do I know if it's squirrels or birds eating my tomatoes?

Birds leave stab-like peck marks in fruit still hanging on the vine, while squirrels take large single bites and often carry fruit away, leaving half-eaten tomatoes on fences or the lawn. Timing helps too: both feed in daylight, but squirrels are the ones you'll see hauling a whole tomato up a fence post.

Why do my tomatoes have black sunken bottoms but no holes?

That's blossom-end rot, a calcium-related disorder caused mostly by uneven watering — not a pest or disease you can spray for. Water deeply on a consistent schedule and mulch the soil, and later fruit on the same plant will usually be fine.

Does netting actually keep animals off tomatoes?

Yes, if it's installed tight. Bird netting stretched over a cage or frame and secured at the base stops birds and slows squirrels considerably. Loose netting fails on both counts — animals reach through it, and birds can become tangled — so keep it taut and anchored.

Related yard clues

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Still not sure? Compare with these clues

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