Among secondary metabolites potatoes contain especially glycoalkaloids that are important in their defence mechanism against different pathogens, such as viruses, bacteria, fungi and insects. On the other hand, these glycoalkaloids are significant toxins in human as well as animal nutrition. In the potatoes the most present glycoalkaloids are alpha-solanine and gamma-chaconine forming as high as 95 % of total glycoalkaloids. The other glycoalkaloids found are beta- and gamma-solanines and chaconines, alpha- and beta-solamarines and aglycones demissidine and 5-beta-solanidan-3-alpha-ol, and in wild potatoes leptines, commersonine, demissine and tomatine. Potato glycoalkaloids are cholinesterase inhibitors and cause poisoning leading to accumulation of acetylcholine in nerve tissue. New varieties have to contain less than 200 mg/kg fresh wt. glycoalkaloids and appreciated are varieties containing 20 to 130 mg/kg fresh wt. glycoalkaloids. The major factors affecting glycoalkaloid content in potatoes are variety, greening, maturity and tuber damage. Because of the significance of these compounds in protection of plants against pathogens, crossing between wild potatoes and standard varieties leads to new hybrids containing less amounts of glycoalkaloids but with their broader structural composition allowing synergistic effect against pathogens.