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[Display omitted] • Assessing variants in non-canonical splicing sites is important during the process of exome sequencing-based primary hyperoxaluria diagnosis. • Capture sequencing-based copy number variant detection should be conducted in patients undergoing exome sequencing to diagnose suspected primary hyperoxaluria. • Exome sequencing will become a standard approach to diagnosing primary hyperoxaluria in pediatric urolithiasis patients. Next generation sequencing-based exome sequencing can be used to identify genetic abnormalities in patients believed to be suffering from primary hyperoxaluria. We outline our efforts to improve the diagnostic capacity of exome sequencing for these patients. We conducted a retrospective analysis of exome sequencing data from 77 pediatric urolithiasis patients with hyperoxaluria of unknown origin. Canonical exome sequencing analysis was performed to identify pathogenic variants in three known primary hyperoxaluria-related genes (AGXT , GRHPR , HOGA1) as per the guidelines of the American College of Medical Genetics. Then, extended exome sequencing analyses of 5′-untranslated region, non-canonical splicing site and copy number variant were performed on patients with negative diagnostic results in these three genes. Canonical exome sequencing analyses led to the diagnosis of primary hyperoxaluria in 20/77 (26%) patients, including eight, four, and eight patients diagnosed with type 1, 2 and 3 primary hyperoxaluria, respectively. Non-canonical splicing site analyses discovered a pathogenic variant in the HOGA1 gene, which led to the diagnosis of six additional patients with type 3 primary hyperoxaluria, while copy number variant analyses from exome sequencing data identified a 1.8 kb copy number loss that impacted the AGXT gene, resulting in the diagnosis of an additional type 1 primary hyperoxaluria case. Extended non-canonical splicing site and copy number variant analyses improve the diagnostic yield of canonical exome sequencing analysis for primary hyperoxaluria from 26% (20/77) to 35% (27/77) in 77 pediatric urolithiasis patients with hyperoxaluria. [ABSTRACT FROM AUTHOR]