A multicommutated flow system was designed and evaluated for the determination of selenium by hydride generation atomic absorption spectrometry (HG-AAS). It was applied to the determination of total selenium in samples of cow's milk (fluid and powder) and infant formulae. Linearity was satisfactory in the range up to 27.5 µg L−1 (h = 0.082 C + 0.0033, h = peak-height, absorbance, C = concentration in µg L−1, r2 = 0.999). Detection (3s) and quantification (10s) limits in solution were LD = 0.08 µg L−1 and LQ = 0.27 µg L−1, corresponding to LD = 3.2 µg kg−1 and LQ = 10.8 µg kg−1 in solid samples, and to LD = 0.8 µg L−1, LQ = 2.7 µg L−1 in fluid milk samples. Trueness was verified by analysis (n = 5) of two reference materials (NIST 1549, Non-fat Milk Powder and NIST 1846 Infant Formula). At the 95% significance level, results were statistically equivalent to the certified values. Instrumental precision (sr(%), n = 5) was in the range 1.4% to 11.7%, analytical precision (sr(%), n = 5) being 4.2 and 9.3% respectively for the determination of the above mentioned reference materials. The sampling frequency of the system was 160 hour−1.