Self-reported food frequency questionnaires (FFQs) have occasionally been used to investigate the association between whole-grain intake and the incidence of colorectal cancer, but the results from those studies have been inconsistent. We investigated this association using intakes of whole grains and whole-grain products measured via FFQs and plasma alkylresorcinol concentrations, a biomarker of whole-grain wheat and rye intake, both separately and in combination (Howe's score with ranks). We conducted a nested case-control study in a cohort from a research project on Nordic health and whole-grain consumption (HELGA, 1992-1998). Incidence rate ratios and 95% confidence intervals were calculated using conditional logistic regression. Plasma alkylresorcinol concentrations alone and Howe's score with ranks were inversely associated with the incidence of distal colon cancer when the highest quartile was compared with the lowest (for alkylresorcinol concentrations, incidence rate ratio = 0.34, 95% confidence interval: 0.13, 0.92; for Howe's score with ranks, incidence rate ratio = 0.35, 95% confidence interval: 0.15, 0.86). No association was observed between whole-grain intake and any colorectal cancer (colon, proximal, distal or rectum cancer) when using an FFQ as the measure/exposure variable for whole-grain intake. The results suggest that assessing whole-grain intake using a combination of FFQs and biomarkers slightly increases the precision in estimating the risk of colon or rectal cancer by reducing the impact of misclassification, thereby increasing the statistical power of the study.