One of three things happens to calories that are ingested: 1) they are used up, 2) they are excreted, and 3) they are stored (generally as fat). Skinny people seem to be able to avoid the third option, so the answer must lie in the first two.
Taking the second one first, it’s possible that their digestive systems just don’t absorb the calories and they pass through. This is the idea behind the new pseudo-fat products like Olestra – it looks like fat, it tastes like fat but it doesn’t digest like fat. It should be unsurprising that the side effects include digestive disruptions. But there are “natural” foods that aren’t well absorbed. These are usually listed as dietary fiber. Vegetables tend to be high in fiber and low in fat so they don’t have many calories to begin with and some of it doesn’t get absorbed.
But, assuming the diet of the skinny person and the, uh, normal person are the same, one possibility is that the skinny person simply absorbs less of the calories taken in.
The first option, burning the calories up, is more frequently cited as the reason for skinniness. Your basal metabolic rate is governed by your pituitary gland, and is largely out of your control. For some people it’s just turned up higher. Also, some skinny people tend to be “higher energy” types, you know, “fidgety”. They just move a lot.
It’s possible to argue which of these factors dominate, but for the most part skinny people just burn more calories. It’s in the genes. It’s not your fault. Have a sundae.
“If ignorance were corn flakes, you’d be General Mills.”
The Straight Dope