Cereals grown world-wide are used as staple food. Due to high temperature, humidity and non-scientific storage prevail the growth of certain species belong to family Aspergillus. Mycotoxins are small (MW ~700), toxic chemical products formed as secondary metabolites by fungal species that readily settle on crops and infect them with toxins in the field or after harvest, during transport and storage. These compounds cause a potential threat to human and animal health through the intake of food products prepared from these commodities. Generally, crops that are stored for more than a few days become a potential target for mould growth and mycotoxin formation. Mycotoxins can occur both in temperate and tropical regions of the world, depending on the species of fungi. The extraction, clean up and analysis methodology for aflatoxins in cereals (maize, rice and wheat) were validated and found it efficient and good in respect of recovery, reproducibility, repeatability, resolution and cost-effective. The extraction solvent (acetonitrile and water) gave ≥ 85% recovery in spiked cereal samples using MycoSep-226 column. The sensitivity (LOD) of HPLC- FLD was higher as compared to HPLC-UV-Vis after derivatization of sample extract with trifluoroacetic acid (TFA). The collected cereals samples from Faisalabad Division, Pakistan exhibited high level of aflatoxins but after treatment with γ-irradiation, more than 95% reduction in AFB 1 and ≥ 97% in Total (∑AFB 1 , AFB 2 , AFG 1 and AFG 2 ) were observed at a dose of 6 kGy. Significant affect of radiation was found in wheat samples because substantial reduction (≥ 95%) was found in AFB 1 and total aflatoxins at high dose of radiation. The level of aflatoxin contamination was far behind that the recommended limits of EU and FDA, USA. From the results it is evident that γ- irradiation is a good technology to remove contaminants like aflatoxins from cereal commodities. The food quality of irradiated cereals was evaluated to study any chemical change in protein (amino acids), fatty acid composition and fungal biomass using different methods. The total biomass (CFU/g) showed linearity behaviour as increasing the dose level of gamma irradiation. In some samples of cereals, no microflora (fungi) was observed after 72 hrs. of incubation. The fatty acidcomposition revealed that linolenic acid and oleic acid showed decrease whereas no significant change was found in other fatty acids. The unsaturated and poly unsaturated fatty acids remained same after γ-irradiation exposure. The amino acids profile showed that leucine, lysine, tryptophane and valine increased while methionine, phenylalanine and threonine decreased in composition as increased the dose level of exposure of gamma irradiation. Overall no major difference was observed in any essential amino acids. The permanent use of contaminated cereals in the area may pose certain diseases like hepatitis, cancer of liver or effect of other major organs of the human body.