Betaine and choline are important components of the one-carbon metabolism cycle, linked with the amino acid homocysteine and lipid metabolism. Analyses of broad ranges of foods point to cereal based foods being important sources of betaine and choline, however to date there has been no detailed analysis of these compounds in cereal flours or cereal products. An analytical method based on optimization of an existing extraction followed by LC-MS/MS analysis was used to analyze 47 plasma samples, 32 cereal flours and cereal fractions, and 51 cereal products. For the method validation LLOQ, recovery, inter- and intraday repeatability were all performed. Whole-grain wheat and rye flours, and products based on these were the best whole cereal sources of betaine (747-1508 microg/g) and to a lesser extent choline (76-159 microg/g), while the bran fraction contained the highest concentrations of betaine and free-choline (2350-2899 microg/g and 366-384 microg/g respectively). Refined wheat flour and products contained lower concentrations, while rice and maize contained only very low and no detectable amounts of betaine respectively (0-10 microg/g), and low amounts of free-choline (<31 microg/g). These results were mirrored in cereal products analyzed, with whole-grain wheat or rye-based cereal products having the highest concentrations of the two metabolites. Plasma concentrations for betaine and free-choline in a group of 47 subjects ranged from 15.2-66.3 and 9.8-18.5 micromol/L respectively, within the range of previous reports. This LC-MS/MS method can be used to rapidly and sensitively quantify betaine and free-choline in plasma and cereal products. Whole-grain cereal products and products containing cereal bran appear to be excellent dietary sources of betaine and free-choline.