In the last two decades, quinoa has gained great popularity in many countries of the world due to its numerous agricultural and medicinal benefits. This paper highlights two objectives: first, to evaluate the differences between three genotypes of quinoa (Chenopodium quinoa Willd.) in terms of crop and chemical characteristics and to study the association between them, and second, to what extent extracts of these genetic constructs may be effective in the treatment of liver cancer. The results indicate that there are significant differences for the tested traits except for globulin (%), 1000 grain weight. The results also indicate that there is a strong positive correlation between the yield, plant height and total protein (%), as well as a strong correlation between protein and both albumin a and albumin b, which enhances the focus on these traits in selecting the distinctive genotype in the grain yield and its protein percentage. HPLC analysis of the ethanol extract of the seeds of the three genotypes revealed that reveals that the major flavonoid and phenolic in chipaya is quercetin (102.20 µg/g) and vanillin (98.32 µg/g) respectively. However, in L14 is naringenin (10.04 µg/g) is the major flavonoid and syringic acid the highest phenolic acid (68.88 µg/g). Concerning the genotype Q5 is hesperetin (22.19 µg/g) is the major flavonoid and chlorogenic acid (78.95 µg/g) the highest phenolic acid. In vitro cytotoxic activity of the three genotypes against hepatocellular carcinoma cell line (HPGE2) indicated that all extracts inhibits the viability and the IC50 of the three Genotypes chipaya, L14 and Q5 were 214.37 ± 3.91, 114.99±0.46 and 113.72 ± 0.87 µg/ml respectively.