To study the intestinal metabolism of lignans, the concentrations of plant and mammalian lignans in intestinal digesta sampled along the intestinal tract of pigs were determined by isotope dilution GC–MS. The pigs were fed rye-bread diets made from either whole rye-grains or rye-grain milling fractions enriched in pericarp–testa, aleurone or endosperm cells. The content and characteristics of dietary fibre varied between diets and had been shown to induce different colon fermentation patterns. As the metabolism of lignans depends on the action of the intestinal flora, we tested whether the rye-bread diets influence the metabolism of lignans. In the ileum, the lignans were mainly present as conjugated plant lignans, which were determined only when the analytical procedure included a hydrolysis step. High recovery of dietary lignans in the ileum may indicate that the lignans enter the enterohepatic circulation. In addition, two to three times the intake of lignans were recovered in the faeces when the diets had a high content of dietary fibre suggesting underestimation of plant lignans in the diet. Most of the plant lignans disappeared from the intestinal tract between the terminal ileum and the caecum. The intestinal concentrations and the disappearance of lignans correlated with the content of lignans in the diet, being highest on the pericarp–testa diet and lowest on the endosperm diet. No effect of fermentation pattern on the intestinal metabolism of lignans was observed. The lignans were liberated from the pericarp–testa diet although the plant cell walls remained largely undegraded.