The use of malonic acid as a complexing agent has enabled a new method to be devised to allow the determination of magnesium to be made using miniaturised isotachophoresis. Using a leading electrolyte of 10 mmol L−1 caesium hydroxide and 2 mmol L−1 malonic acid at pH 5.1 gave the method a high specificity towards magnesium. Investigations using a poly(methyl methacrylate) chip device with an integrated conductivity detector showed that no interference from calcium, strontium, barium and sodium should occur. The method was found to be linear over the range of magnesium concentrations from 0.625 to 75 mg L−1 and the limit of detection was calculated to be 0.45 mg L−1. Separations were demonstrated with water samples but the procedure should also be applicable to more complex sample matrices such as inorganic explosive residues, blood or urine.