Finding a hole in a tomato can be frustrating, but the cause is often simple—pests like hornworms, stink bugs, beetles, birds, or squirrels. Sometimes, internal issues like blossom end rot or temperature changes cause scarring or holes. Small holes without bugs, mold, or odor are usually safe—just cut out the damaged part. If the tomato smells bad or is moldy, discard it. To prevent damage, inspect plants often, water evenly, use netting to deter animals, plant pest-repelling herbs, and keep your garden clean for a healthier harvest.