Tissue level of nitrate and nitrite are established indicators of altered nitric oxide metabolism under various pathological conditions. Determination of these anions in biological samples, in the presence of high chloride concentration, using capillary zone electrophoresis suffers from poor detection sensitivity. Separation conditions providing excellent resolution and submicromolar detection sensitivity of nitrate and nitrite have been developed and validated. Simple sample preparation was applied that maintains nitrite stability in tissue extracts and at the same time allows transient isotachophoresis stacking of the analytes. Nitrate and nitrite concentrations in rat brain and liver tissue samples were determined in control and lipopolysaccharide treated animals.