Background: Gene mutations often result in altered protein expression and, in turn, lead to changes in metabolite levels in one or more distinct biochemical pathways. Traditional analytical methods for metabolite determination are usually time consuming, expensive, and, thus, not suitable for high throughput analysis. However, recent developments in electrospray-tandem-mass-spectrometry allow comprehensive metabolite scanning from very small amounts of blood with high speed, cost effectiveness, and accuracy. Methods: A blood spot from a filter paper equivalent to 3 μl of blood was punched out and transferred to a 96-well microtiter plate. After addition of a set of 14 stable isotope-labeled internal standards, amino acids and acylcarnitines were extracted with methanol. The dried residue was derivatized with butanolic hydrochloric acid and subjected to MSMS analysis. Results: Acyl-carnitines were all determined by a precursor ion scan of 85 Da. Neutral loss scanning of 102 Da was suitable for the quantitation of threonine, serine, proline, histidine, alanine, aspartic acid, glutamic acid, methionine, tyrosine, phenylalanine, isoleucine/leucine and valine. Glycine was detected by a loss of a 56-Da fragment, whereas a 119-Da loss was suitable for the measurement of citrulline, ornithine, arginine, and lysine. Specific problems encountered: owing to their identical molecular weight, isoleucine and leucine could not be quantitated separately, and, owing to their instability, glutamine and asparagine were found to be decarboxylated to their respective acids. Determination was linear over the concentration range tested (20 to 1000 μmol/L), and intraassay and interassay coefficients of variation were in the range of 10–15%. Conclusion: ESI-MSMS proved to be a highly sensitive, linear, and sufficiently precise method for the quantitative determination of amino acids and acylcarnitines in mouse blood, allowing large-scale screening applications when speed and cost effectiveness are mandatory.