Consumption of nut kernels has shown an upward trend due to people's increasing tendency to eat healthy snacks. Pistachio (Pistacia vera L.) is one of the most famous nut trees in the world. The aim of the study is to asses' nutritive value, fatty acid, chemical and sensory parameters, total aflatoxins & aflatoxin B1, and microbiological counts changes after long term storage in freezer (-18±1 °C). Twenty samples of pistachio (raw, unpacked) were collected from the local markets in Egypt. They were subjected to chemical, aflatoxins and microbiological analyses. It was found that pistachio nuts become rancid and not safe to be consumed. It was found that fatty acids profile changed after prolonged storage, where saturated fatty acids increased from 5.77% to 13.57% (+2.35 times), and the unsaturated fatty acids decreased from 47.61% to 41.98% (-11.82%). The most decrease was noticed in unsaturated linoleic acid (-57.84 relative % and -50.20 fats %). Also peroxide value increased. The pistachios nuts after two years of storage at freezing condition were shrinking (moisture content decreased from 5.18% to 4.5%, i.e. -13.13% decreases) resulting in raising the level of relative humidity around the nuts which leads to activation of AFs production. The microbial counts were sharply reduced after long term freezing storage application at refrigerator freezer for 2 years at (-18±1 °C). Staphylococcus aureus was not found in all the pistachio samples. This study has confirmed that prolonged storage render pistachio nuts are a suitable target for deterioration and aflatoxins accumulation, in spite of the reduction of microbial counts was considerable. So prolonged storage must be avoided to reduce deterioration and the threat to human health can be minimized.