Abstract The application of high resolution gas chromatography in combination with low resolution mass spectrometry with electron ionization and MS/MS detection (HRGC-MS/MS) is tested for its use in the analysis of PCDD/Fs in infant formulas. Development of the analytical method was based upon EPA directrices and international recommendations. Calibration linearity was tested and average relative response for any native and labelled compound over the five-point calibration range below 14% was found. The precision and accuracy of the proposed analytical procedure are also presented. Results obtained are in agreement with EPA criteria. The method is applied to the analysis of a number of initial and follow-on milk based infant formulas. In general, HRGC-MS/MS constitutes an interesting method for the analysis of dioxins in such matrices.