Capillary gel electrophoresis was used to characterise 49 Portuguese isolates of potato cyst nematodes, three of Globodera pallida and 46 of G. rostochiensis, and eight isolates representative of pathotypes defined for these two species (Ro1, Ro2, Ro3, Ro4 and Ro5 for G. rostochiensis and Pa1, Pa2 and Pa3 for G. pallida). Protein extracts of four samples of 50 cysts per isolate were separated using a Beckman eCAP SDS 14-200 kit, in a capillary of 57 cm length and 100 μ m internal diameter and with a run time of 40 min. Reproducible protein profiles were obtained and the isolates were compared taking into account the relative migration time and area of each peak recorded by the Gold Software Data System (Beckman). Euclidian distances between isolates were calculated using peak area data and a dendrogram was constructed according to the UPGMA method. Portuguese isolates showed great variability and it seems that protein composition is not related to their geographic origin. Protein profiles of each pathotype were obtained and some of the proteins seem to be specific for each pathotype. However, despite their common reaction to the H1 resistance gene, Ro1 and Ro4 were not grouped together, and Pa1 was not grouped with Pa2.