A two-dimensional capillary isotachophoresis-capillary zone electrophoresis method hyphenated with tandem mass spectrometry was developed and validated for ultrasensitive quantification of serotonin in real human urine samples. Under optimal conditions, the separation was achieved within 12 min (including on-line sample preparation) with the limit of detection of 34 pg mL-1 (due to a large volume sample injection, here 10 µL, and isotachophoretic preconcentration). This concentration limit represents the lowest value for serotonin in comparison to other previously published separation methods employing mass spectrometry detection and applied to urine matrices. Thanks to high orthogonality, on-line concentration and clean-up effects of this approach, other excellent validation parameters such as linearity (coefficient of determination > 0.99), inter-day and intra-day precision (relative standard deviations 3.5-12.2%), accuracy (relative errors within 99-109.4%), and recovery (96-102%) could be easily obtained too. To demonstrate applicability of the method, we monitored serotonin levels in various real samples (from a healthy volunteer and clinical ones). The determined levels, normalized on the creatinine concentrations, were in the range of 6.81-12.86 ng mmol-1 creatinine This advanced method is suggested for an effective, reliable, high sample throughput, and low cost routine clinical screening or targeted metabolomic studies of serotonin in urine samples.