In the three-year field trials (2009)(2010)(2011) at two locations with different altitudes a total of 14 potato cultivars with different colour of flesh (yellow, white, red and purple) were grown. The content of total glycoalkaloids (TGA) was determined by HPLC. TGA content ranged from 18.8 to 102.4 mg/kg fresh matter and none of the cultivars reached the value of risk to human health. Conclusive and decisive influence on the content of the TGA was recorded in genotype. Individual cultivars reached 0.47 to 1.45 of the TGA content in the control cv. Agria. In terms of the colour of the flesh the highest TGA content was found in group of red-fleshed cultivars (1.53 × higher than the average of cultivars with yellow or white flesh); while red-fleshed cv. Rote Emma reached the absolutely lowest TGA content of 14 cultivars, which confirms the decisive role of genotype. On warm, dry habitats in the lowlands a higher TGA content was observed when compared with the amount raised in a typical potato field.