Pistachio kernels contain valuable compounds, of which phenolic compounds and flavonoid compounds are among its most important components. Determining the amount of these compounds in different pistachio cultivars is of particular importance in order to evaluate their nutritional and commercial quality. This study aimed to compare the phenolic and flavonoid compounds of the green skin and kernels of different pistachio cultivars (Shahpasand, Abbasali, Kale Ghoochi, Khanjari, Akbari and Garmeh). The Folin-Cicalteo method was used to measure the amount of total phenolic compounds. Total flavonoids were determined by aluminum chloride colorimetric method. The results showed that the amount of phenolic and flavonoid compounds in the green skin of the tested cultivars was much higher than in the pistachio kernels. There was also a significant difference between the amount of phenolic compounds in the kernels of different pistachio cultivars, and the gallic acid equivalents varied from 39.27 to 66.43 mg/g of dry extract in different cultivars. The amount of flavonoid compounds in the pistachio kernels of different cultivars varied between 0.79 and 1.23 mg of gallic acid equivalent per gram of dry extract. The Garmeh and Akbari pistachio cultivars had the highest amount of flavonoid compounds among the studied cultivars, and its difference with other cultivars was significant at the 5% level. The Garmeh and Shahpasand pistachio cultivars had the highest and lowest amounts of phenolic compounds in both the green skin and the pistachio kernel, respectively, among the studied cultivars.