Automated online and off-line solid-phase extraction (SPE) methods coupled to isotope dilution-high-performance liquid chromatography-tandem mass spectrometry for measuring four isoflavones (daidzein, genistein, equol, and O-desmethylangolensin) and two lignans (enterolactone and enterodiol) in urine are developed. The SPE recoveries for the online SPE method are excellent for most analytes (83-94%) and somewhat lower for enterolactone (61%). The recoveries for all analytes with the off-line SPE method are also very good (65-80%). The limit of detection is lower for the online method (0.1-0.7 ng/mL) than for the off-line method (0.4-3.3 ng/mL). Similarly, the reproducibility is generally better for the online method [coefficient of variation (CV) of 4-12%) than for the off-line method, except for enterolactone, which has a higher CV (18-19%) that is consistent with its lower online SPE recovery. Both methods are adequate for analyzing a large number of samples for epidemiological studies to assess the prevalence of human exposure to isoflavones and lignans.