When something sticks out like a sore thumb, it is obviously and clearly out of place. Like many interesting idioms in English, this phrase is used commonly by people who often do not stop to wonder about its origins. After all, nothing about a sore thumb seems particularly remarkable, so it seems odd to think of something sticking out like one.
Idioms in general are very challenging to language learners, as they rely upon a body of cultural knowledge that may be unfamiliar, and they sometimes use strange sentence structures. The misuse of an idiom can tag someone as a non-native speaker, and as a result, non-native speakers are often more curious than others about peculiar turns of phrase.
People have been describing unusual things with the phrase “it sticks out like a sore thumb” since at least the middle of the 16th century, and the idiom is probably much older. The phrase also experienced a brief heyday in the 1940s, thanks to its appearance in the popular Perry Mason series of detective novels. There are several explanations for why a sore thumb in particular might stick out, as opposed to any other body part.
The first explanation is probably obvious to anyone who has ever injured a limb. When an injury is sustained, the natural instinct is to protect the affected limb, and as a result, a sore thumb is often held at a stiff, odd angle that may be obvious to even the casual observer. This is especially true in the case of a sore thumb that is bandaged, as the bandage will stick out like a flag and make it more difficult to hold the thumb in a natural position. When something sticks out like this, it is difficult to conceal from others, just as it is hard to hide an injury from observers.
In addition to being noticeable to observers, a sore limb also tends to be prone to re-injury when it is held in an awkward position, so it can tend to feel like a gigantic, oversized target. For example, many carpenters have battered fingers that are the result of repeated injuries. The same protective instinct that is designed to cushion an injured limb can actually make it prone to risk, and also more notable; sore thumbs stick out just like limps do, because people change their movements to accommodate them.
There are other colorful ways to say that something sticks out like a sore thumb. For example, people historically have said that something shows up like a mustard pot in a coal scuttle, a reference to the bright yellow color of mustard, which would form a garish contrast against the black color of coal. Many cultures have developed their own distinctive and often fanciful ways to describe something that is clearly out of place, referencing objects and situations that are universally familiar to people in those cultures.