Primary hyperoxaluria type 3 (PH3) is a recently identified inborn error of 4-hydroxyproline metabolism causing kidney stone disease. Diagnosis to date has relied on mutation detection. The excretion of 4-hydroxyglutamate (4OHGlu) was investigated in controls and a cohort of nine patients with PH3 and their parents using flow injection tandem mass spectrometry. 4OHGlu was stable in acidified urine samples and was not influenced by diet. Its measurement was readily incorporated into an existing multi-analyte panel for comprehensive screening for inborn errors of metabolism. There was a steady decline with age in 4OHGlu levels, expressed as μmol/mmol of creatinine, in controls. Levels in patients with PH3 ranged from 6.5 to 98 μmol/mmol of creatinine and were all significantly increased when compared to age-matched controls (<4.2). Levels in eight parents (obligatory carriers of the corresponding mutation) were moderately, but significantly increased, ranging from 0.6 to 2.5 (age-matched controls <1.4, p = 0.03). Urine 4OHGlu screening was used to prospectively diagnose PH3 in an 18-month-old boy with calcium oxalate kidney stone disease associated with hyperoxaluria. 4OHGlu was also increased in a stored newborn screening dried blood spot sample from this child (37 μmol/L, controls <2.53). 4OHGlu testing provides a robust and high-throughput biochemical screen for PH3.