The native potato cultivars 'Michuñe roja' (pink fleshed); 'Michuñe azul' (purple fleshed); 'Cabra' (pink fleshed) and the commercial cultivar 'Désirée' (non-colored fleshed) were stored at 4, 12 and 20°C at 85% RH. At harvest and after 2 and 4 months, dry matter contents, total polyphenol contents (TPC), total antioxidant capacity (TAC) by FRAP, glucose, fructose and sucrose contents, were determined. Colored fleshed potatoes had between two and three times more TPC and TAC than the non-colored with no differences among them. The dry matter content was higher than 20% in all of the genetic materials except in 'Michuñe azul' with 19%. The values of TAC of colored fleshed potatoes were between 300 and 600 mg equivalent Trolox 100 g-1 FW at harvest decreasing both at 2 and 4 months (50% less than harvest value). Potatoes stored at 12°C showed higher TAC compared to those stored at 4 and 20°C that did not show differences. The TPC measured on colored fleshed potatoes were not affected by the storage time and the values were between 300 and 400 mg gallic acid 100 g-1 FW. The potatoes maintained at 20°C presented the highest contents. Glucose levels showed no difference between genetic materials and were not affected by storage temperatures and time (1-1.69 mg g-1 FW). A similar behavior was observed in sucrose (0.94-1.2 mg g-1 FW). Fructose levels were higher in potatoes maintained at 4°C (1.4-1.5 mg g-1 FW) and lower in those kept at 20°C (0.7-0.8 mg g-1 FW) without differences between genetic materials. The colored fleshed potatoes analyzed are rich in functional compounds and represent an interesting alternative for frying. To preserve the functional quality of the raw material it should be stored up to 2 months at a temperature of 12°C.