Qualitative and quantitative detection of paraquat and diquat in urine was performed by capillary zone electrophoresis (CZE). In non-extracted urine, these two closely related herbicides were hydrodynamically or electrokinetically injected into the capillary and well separated in a acidic (pH 3.0) buffer (10 mM glycin, 50 mM NaCl and 20% methanol) within 8 min. The analytes can be identified by their respective migration time with no interfering endogeous compounds around. The peaks were further confirmed by their respective multi-wavelength scanning spectra. Limits of detection (LOD) were 0.2 and 0.1 mg/ml for PQ and DQ, respectively, in nonextracted urine using hydrodynamic injection. Detection sensitivity was greatly improved by solid phase extraction of the compounds followed by CZE using electro-injection under which LODs were 15 and 8 ng/ml for paraquat and diquat respectively. We conclude CZE is a useful method for laboratory diagnosis of herbicide intoxication.