The aim of the study was to evaluate the effect of cultivar, flesh colour, location, year and long-term cold storage on the total anthocyanin content (TAC) in the tubers of 12 potato cultivars with coloured flesh. TAC ranged from 17.0 to 750.1 mg cyanidin/kg fresh matter and was significantly affected by the genotype of the cultivar. The highest TAC was achieved in a three-year average in the cv. Vitelotte (371.0 mg/kg FM, 1.15–8.10 times higher than in the other cultivars). The purple or red colour of the flesh had no significant effect on the TAC. A significantly higher TAC (1.24 times) was determined in the Valečov location with a cooler climate in comparison with the Uhříněves location with a warmer climate. The TAC was significantly influenced by year, the highest values were found at both sites in the year with significant water stress. Storage (4°C, 6 months) significantly affected the TAC in seven out of eight cultivars; the TAC increased in four cultivars and decreased in three cultivars. This is probably due to different disposition of cultivars for the accumulation of sugars during cold storage.