The paper presents the results of a study from 2006-2009, the aim of which was to determine the influence of changing weather conditions in the years of the study and of fertilisation with the biomass of undersown catch crop on the content of harmful substances in the tubers of potato cultivated in the integrated and organic production systems. Two factors were examined: I. Undersown catch crop fertilisation: control (without undersown catch crop fertilisation), farmyard manure, Persian clover, Persian clover + Westerwold ryegrass, Westerwold ryegrass, Persian clover – mulch, Persian clover + Westerwold ryegrass – mulch, Westerwold ryegrass – mulch. II. Production system: integrated and organic. Edible potato was cultivated directly after the undersown catch crop. During the harvest of potato tubers, samples were taken to determine the content of nitrates (V) and glycoalkaloids. The lowest content of harmful substances was recorded in potato tubers harvested in 2007 and 2009, i.e. in years with a favourable distribution of precipitation and temperature. The lowest content of nitrates (V) was characteristic of potato tubers fertilised with Persian clover and the mixture of Persian clover with Westerwold ryegrass, irrespective of the form of their application in both production system, and of glycoalkaloids – of potato tubers fertilised with Persian clover in the form of mulch in the integrated production system.