Holes in apples are most often caused by codling moth larvae, the single most common insect pest of apples worldwide. But birds, yellowjackets, and even internal physiological problems can also create holes or cavities. The type of hole, where it appears on the fruit, and what’s inside it will tell you exactly what happened.
Codling Moth: The Most Likely Culprit
If you’ve cut into an apple and found a tunnel leading to the core, or noticed a small hole on the surface with brown crumbly material around it, you’re almost certainly looking at codling moth damage. The adult moth lays eggs on or near developing fruit, and the newly hatched larva burrows in immediately, sometimes within hours of hatching.
Larvae enter the apple in one of two ways: through the calyx (the indented end opposite the stem) or directly through the side. Side entries are easier to spot because the larva pushes its excrement, called frass, out through the entry hole as it feeds. This brown, granular frass is the telltale sign. On more mature fruit, a reddish ring often forms around the entry point.
Once inside, the larva tunnels toward the center of the apple and feeds primarily on the seeds. These “deep entries” create the classic wormy-apple scenario: a narrow tunnel through the flesh leading to a hollowed-out core. The entry hole gradually enlarges as frass is pushed out, and the same hole often serves as the exit when the mature larva leaves the fruit to pupate. By the time a larva finishes feeding, the hole can be several millimeters wide with a visible trail of brown waste.
Birds and Yellowjackets
Larger, more ragged holes on the surface of apples still hanging on the tree are typically caused by birds or yellowjackets. Bird damage looks like pecking: irregular, relatively shallow gouges in the skin and flesh, often on the sun-facing side of the fruit. These holes tend to be wider and messier than insect entry points.
Yellowjackets create or enlarge holes by chewing directly into the fruit. You’ll often see them clustered inside a cavity they’ve excavated, sometimes alongside ants that arrive afterward to feed on exposed sugars. It’s common to assume the yellowjackets or ants caused the initial damage, but they frequently move into holes that were started by birds or by fruit cracking. That said, yellowjackets are fully capable of chewing through intact skin on ripe apples, especially in late summer when their colonies are large and competing for food.
Internal Cavities Without External Holes
Sometimes you cut open an apple that looks perfectly fine on the outside and find hollow spaces or discolored pockets inside the flesh. This isn’t insect damage. It’s a physiological disorder caused by growing or storage conditions.
Carbon dioxide injury is one common cause. It creates brown, sunken lesions on the skin and discolored cavities within the flesh that can feel dry or spongy. The apple may have a noticeable fermentation smell. Varieties like Honeycrisp, Fuji, Golden Delicious, and Braeburn are particularly susceptible. This type of damage happens in controlled-atmosphere cold storage when CO2 levels get too high, so it’s more likely to show up in store-bought apples that have been in long-term storage than in fruit picked fresh from a tree.
Is It Safe to Eat a Damaged Apple?
An apple with a small codling moth entry hole is not dangerous in itself. The larva and its frass are unpleasant but not toxic. Many people simply cut away the damaged portion and eat the rest. The real concern is what happens after the hole is made.
Any break in the apple’s skin creates an entry point for mold, and certain molds that colonize damaged apples produce a toxin called patulin. This toxin is commonly found in rotting apples and is a particular concern in apple juice made from affected fruit. In humans, patulin exposure can cause nausea, vomiting, and gastrointestinal problems. The World Health Organization notes it is considered genotoxic, meaning it can damage DNA, though a direct link to cancer hasn’t been established. The FDA sets a limit of 50 parts per billion for patulin in apple juice.
For whole apples, the practical rule is straightforward: if the flesh around a hole is firm, white, and smells normal, cutting away the damaged area with a generous margin is reasonable. If the flesh is brown, soft, or has any musty or fermented odor, that fruit has likely been colonized by mold and should be discarded. Don’t use visibly damaged or rotting apples for homemade cider or juice, since patulin can end up concentrated in the liquid even if you can’t see mold.
Preventing Holes in Backyard Apples
Codling moth is notoriously difficult to control because larvae burrow into fruit almost immediately after hatching, which means predators and most biological controls can’t reach them once they’re inside. Sanitation helps reduce populations: pick up fallen fruit promptly, remove any fruit still on the tree that shows signs of damage, and clear debris from around the trunk where pupae overwinter. Wrapping corrugated cardboard bands around trunks in summer can trap larvae seeking a place to pupate, and you can remove and destroy the bands periodically.
The single most effective non-chemical method is bagging individual fruit. This means placing a small paper or mesh bag over each developing apple after fruit thinning, typically when fruitlets are about the size of a marble. It’s labor-intensive, but Utah State University Extension describes it as providing “complete control.” For a backyard tree with a manageable crop, it’s a realistic option. For larger orchards of 10 acres or more, mating disruption using synthetic pheromones is a certified organic practice that can significantly reduce codling moth populations and cut down on the need for insecticides.
For bird and yellowjacket damage, netting draped over the tree is the most practical physical barrier. Harvesting fruit promptly as it ripens also reduces exposure, since both birds and wasps are most attracted to fully ripe or overripe fruit.