5-hydroxytryptamine (5-HT) and its derivatives are endogenously active substances involved in multiple physiological and pathological processes. A novel method of detetermining 5-hydroxyindole ethanol (5-HTOL), 5-hydroxyindole acetic acid (5-HIAA), 5-hydroxytryptophan (5-HTP) and 5-HT in amniotic fluid by gas chromatography-mass spectrometry (GC–MS) was established based on a modified method of derivatization by silanization, in combination with solid-phase extraction pretreatment. Good linearity was achieved in the tested calibration range. The limits of detection (LOD) were 0.05, 0.08, 0.56, 0.43 μg/L for 5-HTOL, 5-HIAA, 5-HTP and 5-HT, respectively. Accuracy (92.4-103.3) and precision (RSD < 5.4%) for all analytes was also determined. Then the method was used to analyze samples of amniotic fluid from 12 patients carrying foetuses with trisomy 21 and 12 healthy controls. Compared with normal fetuses, the levels of 5-HTOL, 5-HTP and 5-HT in the amniotic fluid were significantly altered in the fetuses with trisomy 21 (P < 0.01); the level of 5-HIAA showed no significant difference between the two groups (P>0.05). This is a rapid, sensitive and reliable method for the determination of 5-HTOL, 5-HIAA, 5-HTP and 5-HT, and the study provide both potential trisomy 21 markers and elucidation of the physiological and pathological roles of 5-HT.