Assessing lignin turnover in soil on the basis of a 13C natural abundance labeling approach relies on the assumption that chemical characteristics of labeled and control plant inputs are similar and that the 13C content difference between labeled and control plant inputs is constant within the plant parts. We analyzed lignin in soils, roots, stems and leaves of wheat and maize at different stages of growth using the cupric oxide oxidation method. In both plants, lignin concentrations increased with growth, particularly during grain filling. Maize contained more cinnamyl moieties than wheat. Roots had higher lignin contents (especially cinnamyl moieties) than stems and leaves, and seemed to contribute more to the total soil lignin than the aboveground parts. The isotopic differences (à à13C) of lignin phenols were not significantly different (p > 0.05) between plant organs, confirming assumptions underlying the natural abundance 13C labeling approach. Our data show that lignin content and phenol distribution can vary between plant organs and with the time of harvest. Consequently, the amount of annual lignin input may vary as a function of root amount and harvest date, and thus can affect the calculated apparent turnover times of lignin in natural abundance 13C labeling experiments.