Abstract Globotriaosylceramide is a neutral glycolipid containing the trihexoside Gal( α 1‐4)Gal( ß 1‐4)Glc( ß 1‐1′) covalently bound to N‐acylsphingosine. It was identified as the main storage substance in the kidney of patients with Fabry disease, an X‐linked deficiency of lysosomal α ‐galactosidase A which can significantly be ameliorated by enzyme replacement therapy. Unlike hemizygote males, affected heterozygote females cannot be identified by enzyme assays and therefore may remain untreated. A quantitation of urinary globotriaosylceramides was proposed as an alternative method for their diagnosis. However, the required studies on physiological and pathological variations in the excretion of trihexosides so far have been prevented by a lack of suitable methods. A validated, robust and quick high‐throughput method for the quantitative analysis of globotriaosylceramide isoforms using stable‐isotope‐dilution/internal standardization and electrospray ionization mass spectrometry (ESI‐MS) was developed. An internal standard, stearoyl‐d 35 ‐globotriaosylceramide, was synthesized by enzymatic coupling of d 35 ‐stearic acid to the corresponding lyso‐ceramidetrihexoside. Glycolipid isoforms of high purity were obtained from a 5‐mL urine portion by extraction on C18 solid‐phase columns and a novel washing protocol. ESI‐MS analysis was performed in full and neutral loss scan modes. Urinary trihexosyl‐ and some of the di‐ and monohexosylceramide isoforms can be quantified within a single experiment. All glycolipid isoforms were above detection limit in healthy male and female subjects (n = 63). Prominent elevations of tetracosanoyl‐(C24:0 plus C24:1)‐globotriaosylceramides were found in urines from female (>2.5‐fold above normals) or male Fabry patients (>5.8‐fold above normals), but not among controls. Globotriaosylceramide isoforms shall now be analyzed in Fabry patients, non‐genetic kidney disease and healthy subjects to define the conditions for a safe diagnosis of heterozygotes. Copyright © 2005 John Wiley & Sons, Ltd.