Two kinds of inborn errors of metabolism, dicarboxylic aciduria and hyperoxaluria, have been studied by means of hydroxyl negative ion chemical ionization [NICI(OH)], linked with collisionally activated decomposition experiments on the [M[BOND]H] species of the pathognomonic organic acids. This method has led to non-controversial qualitative determinations of C4–C10 dicarboxylic acids and oxalic, glyceric and glyoxylic acids. NICI(OH) linked with collisionally activated decomposition mass analysed ion kinetic energy spectrometry (CAD MIKES) is proposed herein for diagnostic purposes, as a valid mass spectrometric alternative to standard gas chromatographic/mass spectrometric analysis. The procedure is characterized by simplified sample treatment and by fast execution.