The present study was performed to evaluate the concentrations of phytochemicals (carotenoids and phenolic acids) in wheat varieties grown under comparable organic and conventional conditions over three years as part of a long-term field trial. Phenolic acids of the hydroxybenzoic acid and hydroxycinnamic acid group were quantified by HPLC-DAD after extraction as free, soluble conjugated, and bound forms. Furthermore, the carotenoids lutein and zeaxanthin were determined by HPLC-DAD. There were no statistically significant differences between the two farming systems (sum of carotenoids (microg/g) for 2003, 0.91 +/- 0.55 organic vs 0.96 +/- 0.34 conventional; for 2005, 1.61 +/- 0.22 organic vs 1.33 +/- 0.19 conventional; for 2006, 0.87 +/- 0.33 organic vs 0.83 +/- 0.11 conventional; sum of phenolic acids (microg/g) for 2003, 448.4 +/- 151.1 organic vs 327.3 +/- 232.8 conventional; for 2005, 502.8 +/- 168.3 organic vs 484.4 +/- 111.2 conventional; for 2006, 659.1 +/- 112.5 organic vs 945.9 +/- 353.6 conventional). However, statistically significant year-to-year differences up to 55% were observed. Taken together, these results indicate that climate factors have a greater impact on the phytochemical concentrations in whole wheat than the production method (organic/conventional).