A quantitative, specific, and sensitive method for the determination of N-acylhomoserine lactones (HSLs – a group of bacterial semiochemicals) in the form of their hydrolysis products (N-acylhomoserines, HSs) is presented. Real samples were analyzed by capillary zone electrophoresis-mass spectrometry (CZE-MS) after alkaline lactonolysis and extraction by mixed-mode anion-exchange solid-phase extraction. The presented cleanup significantly speeds up the HSL extraction procedure, strongly reduces sample consumption, and is more selective compared to the commonly used liquid/liquid extraction. Completeness of the hydrolysis reaction was examined by nuclear magnetic resonance spectroscopy. This CZE-MS method complements recently published capillary separation techniques (nano liquid chromatography-MS, partial-filling micellar electrokinetic chromatography-MS, gas chromatography-MS) and provides a possibility to differentiate quantitatively between the homoserines (as naturally occurring degradation products) besides the intact homoserine lactones. The method was found to be quantitative down to a concentration of 0.05 µg/mL (limit of quantification), while the limit of detection was determined with 0.01 µg/mL – sufficient for the analysis of culture supernatants.