The Zellweger spectrum disorders (ZSDs) are characterized by a generalized loss of peroxisomal functions caused by deficient peroxisomal assembly. Clinical presentation and survival are heterogeneous. Although most peroxisomal enzymes are unstable in the cytosol of peroxisome-deficient cells of ZSD patients, a few enzymes remain stable among which alanine:glyoxylate aminotransferase (AGT). Its deficiency causes primary hyperoxaluria type 1 (PH1, MIM 259900), an inborn error of glyoxylate metabolism characterized by hyperoxaluria, nephrocalcinosis, and renal insufficiency. Despite the normal level of AGT activity in ZSD patients, hyperoxaluria has been reported in several ZSD patients. We observed the unexpected occurrence of renal stones in a cohort of ZSD patients. This led us to perform a study in this cohort to determine the prevalence of hyperoxaluria in ZSDs and to find clinically relevant clues that correlate with the urinary oxalate load. We reviewed medical charts of 31 Dutch ZSD patients with prolonged survival (>1 year). Urinary oxalate excretion was assessed in 23 and glycolate in 22 patients. Hyperoxaluria was present in 19 (83%), and hyperglycolic aciduria in 14 (64%). Pyridoxine treatment in six patients did not reduce the oxalate excretion as in some PH1 patients. Renal involvement with urolithiasis and nephrocalcinosis was present in five of which one developed end-stage renal disease. The presence of hyperoxaluria, potentially leading to severe renal involvement, was statistically significant correlated with the severity of neurological dysfunction. ZSD patients should be screened by urinalysis for hyperoxaluria and renal ultrasound for nephrocalcinosis in order to take timely measures to prevent renal insufficiency.