A comparison between electrospray ionization (ESI) and the recent introduced atmospheric pressure photo-ionization (APPI) technique is described for the liquid chromatography/mass spectrometric (LC/MS) determination of aflatoxin B1, B2, G1 and G2 in food. For the optimization of APPI, several APPI ion source parameters were examined. Furthermore, the chemical noise and signal suppression of ESI and APPI by sample matrix interference were investigated. The results indicated that APPI has the low chemical noise and the little signal suppression in comparison with ESI. The mean recovery of each aflatoxin from peanuts, corn, nutmeg and red pepper sample spiked at 1 ng g(-1) ranged from 89 to 105% with relative standard deviations of 3.3-5.1%. The limit of detection (S/N = 3) in all food was in the range 0.11-0.5 ng g(-1). From these studies, it is suggested that APPI can be used as an additional tool in food residue analysis.