A high-throughput agarose gel electrophoresis (AGE) analytical method has been developed to separate lignin fractions according to their molecular weight (M w), charge, and shape. Operating conditions to effect separation of species have been evaluated along with imaging parameters. Kraft, soda (Protobind), and Organosolv lignins showed distinct differences in migration. Bands were cut, extracted, and cross-analyzed by gel permeation chromatography (GPC), 1 H NMR, and pyrolysis GC/MS to confirm their identity as lignin. The band intensity was correlated with lignin concentration by running serially diluted samples and imaging each lane to produce a precise calibration curve. The AGE technique was used to monitor and compare enzymatic, bacterial, chemical, and hydrothermal lignin digestions. Each method showed changes in lignin migration and band intensities over time. Low M w species were seen in samples collected from the anode buffer tank. Though requiring further development, the AGE method can provide structural information about the lignin and is accessible to biological and chemistry laboratories.