Kanihua (Chenopodium pallidicaule Aellen) is a Chenopodiacea of the andean region, that contains between 15 and 19% protein, with essential amino acids. The objective of the study was to fractionate and electrophoretically characterize the proteins of kanihua seed varieties Cupi-Sayhua and Ramis. In the whole meal, the proximal analysis and fractionation were performed, and the flour was fractionated by five techniques according to Osborne solubility to obtain albumins, globulins, prolamins and glutelins. The methodology, solvents and extraction time were optimized; and the electrophoretic profiles of the fractions were identified. The highest protein content (p≤ 0.05) was of kanihua flour and its protein fractions, compared to kiwicha and wheat. The highest percent yield (p≤ 0.05) during 1 h of sequential extraction of the protein fractions, was obtained with the Rodriguez y et.al., technique for albumins and glutelins, and with the technique described by Barba de la Rosa y et.al., for globulins and prolamins. The following results were found in Ramis and Cupi-Sayhua kanihua: albumins: 15.4±0.3 and 15.8±0.3%, globulins 7S: 24.1±0.5 and 26.3±1.0%, globulins 11S: 25.7±1.0 and 26.7±1.0%, prolamins: 9.6±0.1 and 9.9±0.5% and glutelins: 22.9±0.1 and 21.5±1.4%, respectively. The electrophoretic profile showed patterns similar in number of bands and differences in concentration in both varieties.