The optimization and validation of a protocol for the quantification of six dietary lignans, i.e., secoisolariciresinol, matairesinol, lariciresinol, pinoresinol, medioresinol, and syringaresinol, in food are presented. The method incorporates isotope dilution to ensure correct accuracy and precision, introducing the utilization of individual stable 13C3-labeled lignans. To demonstrate the potential of this new method, preliminary results of the levels of dietary lignans in selected foods are presented. It is concluded that the method fulfils the reliability criteria and can be applied to the analysis of the most common lignans in human food, being an essential asset to establish the intake of lignans in a determined population and their relation with disease prevention.