Potato can be a valuable source of antioxidants in the human diet, and genetic variability exists for antioxidant contents. The present study was carried out to evaluate the extent of variability in coloured flesh potatoes from andigena clones. There were significant differences among clones in ascorbic acid, phenols, total carotenoids and anthocyanins. During the two crop seasons, purple fleshed andigena potato clone JEX/A-122 was found to be superior in ascorbic acid, phenols and anthocyanins, followed by JEX/A-121. However, total carotenoids content in all the evaluated clones in general was less than half to that of yellow fleshed control variety Kufri Surya. Tuber dry matter in JEX/A-121 and JEX/A-122 was moderate (19.6 %) and statistically at par with that of Kufri Surya (21.1 %). Effect of growing season was also noticed on antioxidants status. The clones JEX/A-121 and JEX/A-122, superior in antioxidants showed significantly lower biological yield (226 and 246 g plant−1) as compared to commercial varieties Kufri Surya and Kufri Pukhraj (661 and 665 g). Tuber yield in JEX/A-121(166 g plant−1) and JEX/A-122 (156 g plant−1) was also significantly lower than the variety Kufri Surya and Kufri Pukhraj (410 and 416 g plant−1). The poor plant canopy and low yield in these clones was attributed to low leaf area, early senescence and reduced photosynthesis efficiency. Lower productivity in these clones negates the possibility of their direct exploitation towards either nutrient enhancement in potato driven food chains or as natural colourants. The genetic variability reported in this paper, however, provides impetus for future breeding work directed specially at enhancing the antioxidative matrix by targeted selections.