To characterize phytonutrients, the seeds of 12 purple Perilla (Perilla frutescens var. crispa) accessions collected from Korea and Japan were used for quantitative analysis of tocopherols, phytosterols, squalene and fatty acids. The average tocopherol, squalene and phytosterols contents were 12.2 mg $100g^{-1}$, 3.99 mg $100g^{-1}$ and 77.20 mg $100g^{-1}$, respectively. Among 4 tocopherol (T) isomers (${alpha}$-T, ${eta}$-T, ${gamma}$-T, and ${delta}$-T), ${gamma}$-T was present in the highest quantity (11.03 mg $100g^{-1}$) with the least variation (CV = 13.7%), while ${eta}$-T was present in lowest quantity (0.25 mg 1$100g^{-1}$). Compared to campesterol (4.36 mg $100g^{-1}$) and stigmasterol (13.32 mg $100g^{-1}$), ${eta}$-sitosterol exhibited higher quantity (59.51 mg $100g^{-1}$) with 9.5% of variation. The major fatty acids were unsaturated fatty acids such as linolenic (61.5%), linoleic (17.3%), and oleic (9.9%) acids compared to saturated ones: palmitic (7.6%) and stearic (3.7%) acids. When Korean and Japanese accession were compared, almost no difference in content could be observed, while more variation as evaluated by CV (%) could be observed in Japanese accession in most phytonutrients suggesting wider genetic variation of purple Perilla in Japan. Presence of all above-mentioned phytonutrient compounds strongly suggested health beneficial value of purple Perilla seeds.