The coupling of a flow system to a household microwave oven is proposed for on-line urine sample decomposition with posterior off-line Ca and Mg determination by flame atomic absorption spectrometry (FA-AS). The variables investigated in the optimisation of the decomposition process were: HNO3 concentration (0 - 2.0 mol L-1), sample injection volume (150 - 400 mul), microwave power (0 - 6 min) and microwave actuation time (0 - 6 min). Based on the sample volume injected into the flow system and the power effect, the best results achieved for Ca and Mg were 200 mul for injected sample volume, maximum microwave power (659 W) and 1 min of microwave actuation. The use of 1 mol L-1 HNO3 concentration was efficient, being a less drastic condition for decomposition process, minimising the environment contamination and the use of nitric acid. The proposed method presented an acceptable precision for calcium (expressed as RSD) of 1% (n = 12) for repeatability and 11% (n = 10) for reproducibility. For magnesium, the precision was 3% (n = 12) and 11% (n = 1), for repeatability and reproducibility, respectively.204243249