An optimization of the hydride generation quartz furnace atomic absorption spectrometry (HG-QFAAS) method used for selenium trace determination was performed. Experimental designs at two levels, including seven factors, were used, allowing the evaluation of the influence of each analytical variable on peak area, repeatability and signal-to-noise ratio (S/N). For peak area, the most significant factors are the helium and oxygen flow-rates. The NaBH4 flow-rate and hydride generator temperature have a strong significant effect on repeatability. No factor is really essential for the S/N. The detection limit is 1.5 ng of SeIV(3sb). The absorbance is found to be linear over the range 1.5–60 ng. A 3.72% relative standard deviation is obtained for six determinations of 10 ng of SeIV standard solution. A Community Bureau of Reference (BCR) certified reference material (CRM) 402 White Clover was studied, in order to control the quality of the determination. The total selenium contents were determined using the HG-QFAAS optimized method and then compared with the results given by an electrochemical method (differential pulse cathodic stripping voltammetry).