The quality of potatoes from organic and conventional farming was investigated in this study. Tubers of eight potato varieties, organically and conventionally produced at one or two geographical sites in controlled field trials, were collected in four consecutive harvests from 1996-1999. The parameters analysed included nitrate, trace elements (As, Cd, Co, Cu, Fe, Hg, Mn, Ni, Pb, Se, Zn), vitamin C, potato glycoalkaloids, as well as chlorogenic acid, polyphenol oxidase and rate of tuber enzymic browning. The results indicated lower nitrate content and higher vitamin C and chlorogenic acid content to be the parameters most consistently differentiating organically from conventionally produced potatoes. Elevated concentrations of glycoalkaloids were also observed throughout the experiments in some potato varieties grown in organic farming systems. Principal component analysis (PCA) of the analytical and other data using three PCs confirmed a good separation between the organically and conventionally produced potatoes when studied in single crop years. However, score-plots (objects) and loading-plots (variables) of pooled results from the consecutive harvests showed that between the years' changes and also variety as well as geographical variations are equally or more important factors determining the quality of potatoes than the farming system. Further studies of various marker compounds of potato quality related to the organic or conventional farming systems should be performed before unbiased information can be given to the consumers.