Abstract: To evaluate the uncertainty in determination of total arsenic and total mercury in apple by atomic fluorescence spectrometry. The influence factors of uncertainty in the cource of determination were analyzed and considered. According to mathematical model,the components of uncertainty and the combined uncertainty were calculated. The concentration of total arsenic and total mercury in apple was respectively 5.256 and 189.750 μg/kg. The relative expanded uncertainty of total arsenic and total mercury was 14.694% and 6.748% respectively,and the result of the measurement was (5.256±0.772)and(189.750±12.804) μg/kg respectively.The different concentration point of the standard curve should be correctly chosen to evaluate the different concentration of sample;the repeated times of measurement and the stability of the instrument should be increased;the method and pipetting device of configuration standard soution shoule be reasonability chosen. Those factors are very important. The relative expanded uncertainty of total arsenic is smaller than the expanded uncertainty of total mercury. The measured values of total arsenic is closer to the truth than the measured values of total Mercury.