Breeding efforts have been undertaken to increase resistance of maize to fusarium ear rot (FER) and to fumonisin accumulation. Flavonoids in the pericarp of the kernels are considered particularly able to reduce the fumonisin accumulation. The aim of this 2-year field study was to assess the effect of flavonoids on FER symptoms and fumonisin contamination in maize kernels using two isogenic hybrids, one providing pigmentation in the pericarp (P1-rr) and the other without it (P1-wr). FER incidence (FERi), FER severity (FERs), the incidence of infections caused by Fusarium spp. in symptomless kernels (FF) and fumonisin contamination (FUM) were assessed in both hybrids. Significant differences between the two hybrids were detected mainly in 2012 trials where P1-rr showed lower FERi (P < 0Á01), FF (P < 0Á05) and FUM (P < 0Á1) than P1-wr. Site, characterized by local temperature and precipitation, played a relevant role in modelling all the measured variables, as its effect was highly significant in both years, whether they were considered individually or altogether. The interaction of hybrid with location was a significant (P < 0Á001) source of variation only for FF. FF, together with FERi, was also significantly (P < 0Á001) influenced by the interaction of hybrid with year. In general, FUM was more influenced by year and location parameters, such as temperatures during late ripening, than by flavonoid presence in kernel pericarp. The results indicate that flavonoid pigments alone may not be an important component in the resistance of maize to fumonisin accumulation.