Background The primary hyperoxalurias are inherited disorders of glyoxylate metabolism that lead to overproduction of oxalate, urolithiasis and renal failure. Delays in diagnosis can be costly in terms of preserving renal function. Here we present a rapid liquid chromatography tandem mass-spectrometry screening method for the analysis of metabolites (primary hyperoxaluria metabolites) produced in excess by primary hyperoxaluria patients that include glycolate, glycerate and 2,4-dihydroxyglutarate. Methods Assay performance was compared to our existing gas chromatography–mass spectrometry method and clinical utility established by analysis of urine samples from patients with confirmed primary hyperoxalurias (11 PH1, 12 PH2 and 8 PH3) and controls ( n = 12). An additional 67 urine samples from patients with PH3 were used postvalidation to confirm the derived 2,4-dihydroxyglutarate cut-off. Results Glycolate, glycerate and 2,4-dihydroxyglutarate showed a mean bias of 3.3, −22.8 and 5.7%, respectively, compared to our previously published gas chromatography–mass spectrometry method. The mean total imprecision for glycolate, glycerate and 2,4-dihydroxyglutarate was shown to be 6.4, 10 and 11%, respectively. Clinical assessment confirmed that mean urinary glycolate, glycerate and 2,4-dihydroxyglutarate excretion were significantly elevated in patients with PH1, PH2 and PH3, respectively. The greatest sensitivity and specificity for PH1, PH2 and PH3 was achieved at cut-offs of 193, 100 and 4.9 μmol/mmol for glycolate, glycerate and 2,4-dihydroxyglutarate, respectively. Conclusions A rapid screening method for the identification and differentiation of patients with suspected PH1, PH2 and PH3 is presented that allows focussing of genetic testing, saving time, money and, with earlier treatment, potential preservation of renal function for these patients.