The high nutritional potential of native potatoes makes them an invaluable genetic resource for breeding. However, pathogens have caused both yield and industrial quality losses, and plant tissue culture is a promising alternative to obtain clean plant material. We compared distinct segments excised from apical and lateral sprouts taken from tubers as initial explants for in vitro culture of sixteen native potato genotypes. Thus, apical-distal (AD), mid-apical, lateral-distal, and mid-lateral segments were all grown on Murashige & Skoog medium. These explants were aseptic, reactive, and viable for all genotypes (with a probability greater than 30%), yielding cumulative proliferation rates of up to 1:10 individualizable segments, and about 86% of in vitro plants with 2 to 11 roots of up to 117 mm long. Responses were genotype-dependent during all stages of cultivation, and the best responding genotypes were Maravillosa, Duraznillo and Pepina Rodeo. On the other hand, AD sprouts were the best sprout type and segment for in vitro establishment, regardless of genotype. This is the first study of its kind with such a large range of Andean potato genotypes and should contribute to their germplasm conservation and increased multiplication efficiency.