The content and biological activity of patatin and the protease inhibitors of molecular size 20-22 kDa present in whole potato tubers were investigated as a function of storage time. The amount of buffer-extractable protein decreased gradually during storage of whole potatoes of the cultivars Bintje and Desiree for 47 weeks whereas, for Elkana, it increased after approximately 25 weeks. The patatin proportion of the extractable protein did not decrease significantly during storage, whereas the proportion of PP20-22 protease inhibitors decreased. All cultivars contained several different patatin isoforms. Bintje and Desiree showed patatin populations with two masses whereas for Elkana, only one molar mass was found. Patatin isoforms of the three cultivars examined showed no significant differences in stability towards degradation as was concluded from capillary electrophoresis analysis. No inactivation of patatin or protease inhibitors by partial degradation of these proteins was observed using matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS), whereas enzyme-activity assays suggested that the biological activity, especially in the cultivar Bintje, decreased markedly at the break of dormancy.