The expanding demands of consumers requires food quality control to be improved all the time. Higher concentration of biogenic amines can lead to food toxicity, for example they can cause migraine headaches in people who consume products rich of serotonin or tyramine. Methylxanthines (caffeine and metabolites) can also have side effects to human comfort – high doses can lead to unrest, irritation or insomnia. Most vitamins are supplied to humans only as a part of food meals or dietary supplements. Knowledge about their concentration in food can be useful for composing various diets. In this work specification of complete sample preparation parameters for extraction of the compounds from food matrices has been reviewed. Particular attention was given to the preparation stage as well as to extraction methods that have been used. The second part of the work presents data from chromatographic methods for determination and separation of selected biogenic amines, methylxanthines and water-soluble vitamins in food. Stationary and mobile phases, detection methods as well as validation data have been reviewed. This publication is a comprehensive compendium of analytical procedures for food analyses of the previously mentioned compounds.