Organic acids analysis is a powerful technique in the diagnosis of inborn errors of metabolism. Clinically, patients present with severe symptoms, and early detection and appropriate treatment are often lifesaving. Most of the existing methods are based on gas chromatography in combination with mass spectrometry and require sophisticated equipment and complex sample pretreatment and derivatization. We propose a rapid, simple, and automated capillary electrophoretic method for routine analysis of urine to detect 27 organic acids related to metabolic diseases. With this method, direct measurements are performed on samples after initial centrifugation and dilution, if needed. Separation is performed in pH 6.0 phosphate buffer with methanol added as an organic modifier, -10 kV applied potential, and ultraviolet detection at 200 nm. The assay is completed in <15 min, and alternative separation conditions are proposed in case of overlapping peaks. The developed method allows the identification and quantitation of methylmalonic, pyroglutamic, and glutaric acids in samples of patients with diseases related to these acids.