In order to investigate exposure end effect markers of fruit and fruit fibre intake we investigated how fresh apple or apple-pectin affects the urinary metabolome of rats. Twenty-four Fisher 344 male rats were randomized into three groups and fed a standard diet with different supplementations added in two of the groups (7% apple-pectin or 10 g raw apple). After 24 days of feeding, 24 h urine was collected and analyzed by UPLC-QTOF-MS in positive and negative ionization mode. Metabolites that responded to the apple or pectin diets were selected and classified as either potential exposure or effect markers based on the magnitude and pattern of their response. An initial principal component analysis (PCA) of all detected metabolites showed a clear separation between the groups and during marker identification several new apple and/or pectin markers were found. Quinic acid, m-coumaric acid and (-)epicatechin were identified as exposure markers of apple intake whereas hippuric acid behaved as an effect marker. Pyrrole-2-carboxylic acid and 2-furoylglycine behaved as pectin exposure markers while 2-piperidinone was recognized as a potential pectin effect marker. None of them has earlier been related to intake of pectin or other fibre products. We discuss these new potential exposure and effect markers and their interpretation.