The oil fractions of Amaranthus caudatus L. and Amaranthus cruentus L. seeds were studied after different treatments of the seeds. The oil contents were 7.1 and 8.5% for raw A. caudatus L. and A. cruentus L. seeds, and consisted of 80.3–82.3% of triacylglycerols (TAGs). Phospholipids represented 9.1–10.2% of the oil. The squalene content was 4.8–4.9% in both types of oil. Air classification increased the lipid content and decreased the content of squalene, while heating (popping and cooking) increased the squalene content. After germination, the lipid fraction was decreased in their TAGs and increased in their phospholipids. The main fatty acid composition (palmitic, linoleic and oleic) was not affected by thermal treatments or by germination of the seeds. The hydroperoxide stability test showed that the stability of amaranth oil was more than that of sunflower oil.