Background: Food contamination with fungi and the production of mycotoxins, such as aflatoxin, allow the toxins to enter human body. Continuous contamination with low doses of these agents can act as a major risk factor for hepatocellular carcinoma. Thus the present study was carried out to evaluate the detection of contamination in eggs with aflatoxin by PCR method.Materials and Methods: In a cross-sectional study, a total of 144 suspicious and 211 intake eggs were collected and three samples of fungi including aspergillus niger, penicillium expansum, and fusarium verticillioides as negative controls and 14 samples of aspergillus flavus as positive controls were selected and examined using TLC and PCR. The results were analyzed through SPSS software. Results: By PCR, neither aflR, omt-A, and ver-1, nor-1 was detected in intake eggs by PCR. Of the suspected eggs, four samples with nor-1, two samples with aflR, and two samples with omt-A could be detected. Three samples of the 14 strains of aspergillus flavus were shown to be positive through the use of TLC and the four primers. One strain of aspergillus flavus was positive with all of the four primers; however, it was negative in TLC.Conclusion: The findings of this study indicated that PCR is a sensitive, fast, and specialized technique, but it cannot detect the presence of the fungi before the appearance of colonization. Thus for indicating toxcification, other complementary tests are also required.