In this study, the effects of wet and microwave digestion methods for the determination of cupper (Cu), iron (Fe), and zinc (Zn) in standard reference materials (SRMs) and food samples by using flame atomic absorption spectrometry (FAAS) were investigated. HCl, HNO3, and HNO3 + H2O2 mixture were applied to the digestions of the SRMs (IRMM-804 rice flour, GBW 10010 rice, GBW 10011 wheat flour, 1567a wheat flour and 1571 orchard leaves) for optimization and validation of the method by using wet and microwave digestion systems. Concentrations of Cu, Fe and Zn in SRMs were determined by FAAS, and the lowest percent relative errors of analytes (from -2.5 % to +3.0 %) were obtained by using HNO3 + H2O2 mixture in the microwave digestion. Limit of detection (LOD) and limit of quantification (LOQ) values for analytes obtained by using HNO3 + H2O2 mixture in the microwave digestion were 14.5 and 48.3 mu g L-1 for Cu, 16.4 and 54.6 mu g L-1 for Fe, and 10.8 and 36.0 mu g L-1 for Zn, respectively. The concentrations of Cu, Fe and Zn in food samples such as wheat flour, corn flour, rice flour and tahini were determined by FAAS using the HNO3 + H2O2 mixture in both wet and microwave digestion systems. It was observed that the results obtained with microwave digestion were higher than those of wet digestion. The concentrations of Cu, Fe and Zn in samples found by microwave digestion were compared with the maximum permissible values given in the Turkish standards, regulations and some literature values.