Fractional factorial design was utilized to evaluate the effect of combinations of nitric acid, hydrogen peroxide, hydrochloric acid and water for microwave digestion of fish muscle. Upon digestion, copper, iron and zinc were determined by flame atomic absorption spectroscopy. H2O2 and HCl volumes were found to be the most significant parameters which resulted in good metal recoveries. This is especially so for the effect of HCl on Fe recovery. The results indicated that the combination of 4 mL 65% HNO3, 2 mL 30% H2O2 and 2 mL 30% HCl gave the most satisfactory percentage recovery. There was good agreement between measured and certified values for all metals with respect to the DORM-3 fish protein.