Amaranthus (Amaranthus caudatus L.) is the richest source of squalene among all plants. Squalene is used as a component of some adjuvants in vaccines for enhancement of the host immune response. Squalene content was estimated by high-performance liquid chromatography and amino acids profiling was performed using an amino acid analyzer. Squalene content, up to 7.66%, was found in the raw seeds of amaranthus, which was further enhanced to 8.13% by popping. The results revealed that amaranthus populations have wide significant variations (p < 0.05) in 1000 seed weight (0.61-1.13 g), protein content (11.50-19.80%), total phenols (4.36-7.82 µg GAE/mg sample), total flavonoid (0.70-2.32 mg QE/g dw), and squalene (3.23-7.66% in raw seeds and 3.38-8.12% in popped seeds). Genotypic variability in amino acids composition, viz. lysine (4.96-5.90%), arginine (8.48-8.80%), leucine (5.20-6.70%), valine (3.60-4.60%), phenylalanine (5.30-8.00%), methionine (3.08-4.97%), tyrosine (5.92-7.96), threonine (3.20-4.32%), and glycine (6.60-8.20%), was also observed. Wide genetic variability in amaranthus grains may be used for improved varietal development breeding programs. It can be further concluded that an increase of squalene content in amaranthus grains by heat treatment could be helpful to fulfil the demands of cosmetic and pharmaceutical industries, especially with respect to vaccine production against virus-generated pandemics.