Purpose To determine whether (poly)phenols from gastrointestinal-digested green pepper possess genoprotective properties in human colon cells and whether the application of a culinary treatment (griddling) on the vegetable influences the potential genoprotective activity. Methods (Poly)phenols of raw and griddled green pepper (Capsicum annuum L.) submitted to in vitro-simulated gastrointestinal digestion were characterized by LC-MS/MS. Cytotoxicity (MTT, trypan blue and cell proliferation assays), DNA damage and DNA protection (standard alkaline and formamidopyrimidine DNA glycosylase (Fpg)-modified comet assay) of different concentrations of (poly)phenolic extracts were assessed in colon HT-29 cells. Results A total of 32 (poly)phenolic compounds were identified and quantified in digested raw and griddled green pepper. Twenty of them were flavonoids and 12 were phenolic acids. Griddled pepper doubled the (poly)phenol concentration compared to raw; luteolin 7-O-(2-apiosyl)-glucoside and quercitrin constituted the major (poly)phenols in both extracts. Raw and griddled pepper (poly)phenolic extracts impaired cell proliferation and induced low levels of Fpg-sensitive sites, in a dose-dependent manner, even at a non-cytotoxic concentration. None of the concentrations tested induced DNA strand breaks or alkaline labile sites. Nor did they show significant genoprotection against the DNA damage induced by H2O2 or KBrO3. Conclusions Green pepper (poly)phenols did not show genoprotection against oxidatively generated damage in HT-29 cells at simulated physiological concentrations, regardless of the application, or not, of a culinary treatment (griddling). Furthermore, high concentrations of (poly)phenolic extracts induced a slight pro-oxidant effect, even at a non-cytotoxic concentration.