CZE was investigated for separation of lysergic, iso-lysergic, and paspalic acid. BGEs were optimized regarding separation selectivity and analysis time as well as MS compatibility. BGEs using asparagine, Na-tetraborate, or ammonium acetate yielded satisfactory resolution when 40% of methanol was added and the pH adjusted to 8.3. Applying acidic BGEs also allowed fast separations but the poor stability under acidic conditions of the selected analytes prevented further use. With ultraviolet (UV) detection, LODs were 0.45 and 0.40 mg/L for paspalic acid and lysergic acid, respectively. Run-to-run precision of peak areas was 1.8% for lysergic acid and 1.9% for paspalic acid and day-to-day precision was 2.4 and 4.0%, respectively. When MS detection was used LODs improved to 0.09 mg/L for paspalic acid and 0.07 mg/L for lysergic acid. Repeatability results were excellent for a CZE-MS method without internal standard ranging from 3.4% for the highest standard concentration to 5.8% for the lowest concentration. Recovery and matrix effects were studied with samples taken from different stages of the manufacturing process and yielded an average recovery of 100.8% and a RSD of 5.7%.