Prenatal diagnosis is available for many lysosomal storage disorders (LSD) using chorionic villus samples or amniocytes. Such diagnoses can be problematical if sample transport and culture are required prior to analysis. The purpose of this study was to identify useful biochemical markers for the diagnosis of lysosomal storage disorders from amniotic fluid. Amniotic fluid samples from control (n=49) and LSD affected (n=36) pregnancies were analysed for the protein markers LAMP-1 and saposin C by ELISA, and for oligosaccharide and lipid metabolite markers by electrospray ionisation-tandem mass spectrometry. Lysosomal storage disorder samples include; aspartylglucosaminuria, galactosialidosis, Gaucher disease, GM1 gangliosidosis, mucopolysaccharidosis types I, II, IIIC, IVA, VI, and VII, mucolipidosis type II, multiple sulfatase deficiency, and sialidosis type II. Each disorder produced a unique signature metabolic profile of protein, oligosaccharide, and glycolipid markers. Some metabolite elevations directly related to the disorder whilst others appeared unrelated to the primary defect. Many lysosomal storage disorders were clearly distinguishable from control populations by the second trimester and in one case in the first trimester. Samples from GM1 gangliosidosis and mucopolysaccharidosis type VII displayed a correlation between gestational age and amount of stored metabolite. These preliminary results provide proof of principal for the use of biomarkers contained in amniotic fluid as clinical tests for some of the more frequent lysosomal storage disorders causal for hydrops fetalis.