Three varieties of native potato (Imilla blanca, Imilla negra and Loc'ka) that grow in the Andean region at more than 3800 m.a.s.l. were selected fot the extraction and characterization or their starch. Instrumental techniques such as scanning electron microsocopic (SEM), differential scanning calorimetry (DSC), Fourier transformed infrarred spectroscopy (FTIR), X-ray diffraction, colorimetry and polarized light microscopy were used. The results showed that only Loc'kás starch had a unimodal granule size distribution, whereas Imilla negra and Imilla blanca starches showed two and three granule size populations, respectively. The starch from Imilla negra showed higher apparent amylose content, peak viscosity, phosphorous content and paste clarity. The starch from Imilla blanca showed high relative crystallinity, while Imilla blanca and Imilla negra had higher intensity ratios than that from Loc'ka, suggesting high molecular order. Cooked starch from Imilla negra showed higher resistant starch (RS) fraction than the other starches studied.