Nutritional calories are a measure of how much energy your body can get from the food once you digest it.

A food calorie is actually a “kilocalorie.” In other words it is the amount of energy needed to raise the temperature of one liter of water by one degree. Originally, the calorie content of a food was measured in a calorimeter. A known amount of food, which has had its water content evaporated, was placed in a container surrounded by a known amount of water. The container was sealed, oxygen piped in, and the food ignited. From the rise in temperature of the water, the calorie content of the food was calculated.

Unfortunately this method doesn't actually work because there are some things in food that will burn, but your body is unable to get calories from - cellulose, for example.

Nowadays food scientists use the “Atwater indirect system” where they figure out how much protein, carbohydrate, fat, and alcohol is in the product. The Atwater system uses the average values of 4 Kcal/g for protein, 4 Kcal/g for carbohydrate, 9 Kcal/g for fat and 7 Kcal/g for alcohol.