Introduction Very-early-onset inflammatory bowel disease is associated with an increased rate of immune dysregulation. A 14-year-old male with Crohn's and recurrent liver abscesses had 2 dihydrorhodamine (DHR) oxidative burst and phorbol myristate acetate (PMA) induced assays reported as normal. Case Description The patient had gastrointestinal symptoms since infancy and was diagnosed with Crohn's disease at 6 years. He had recurrent sinopulmonary infections and 2 liver abscesses. Two prior DHR assays were reported as normal based on percentage of neutrophils demonstrating oxidative burst (84%, 73%), without reporting NADPH oxidase (NOX) activity measured by mean fluorescence intensity (MFI). Due to high suspicion for chronic granulomatous disease (CGD), a third oxidative burst was obtained from another reference laboratory. It revealed significantly reduced NOX activity in neutrophils. Flow cytometry for NADPH-oxidase specific proteins showed normal expression of gp91phox, p22phox, p67phox and p40phox and absent p47phox. The patient had a heterozygous NCF1 delta GT mutation and a wild-type second allele. He underwent successful hematopoietic stem cell transplantation from a fully matched unrelated donor. Discussion DHR assay is the standard diagnostic test for CGD. However, complete interpretation requires both MFI and percentage of positive cells, and variability exists in how DHR is performed and reported by different reference laboratories. This patient's diagnosis and treatment were delayed by a lack of recognition of abnormal test results. It is essential for ordering physicians to understand the test, including performance characteristics, analysis and reporting by laboratories. Further, specific protein flow can be used to confirm an abnormal DHR result enabling rapid genetic triage. Very-early-onset inflammatory bowel disease is associated with an increased rate of immune dysregulation. A 14-year-old male with Crohn's and recurrent liver abscesses had 2 dihydrorhodamine (DHR) oxidative burst and phorbol myristate acetate (PMA) induced assays reported as normal. The patient had gastrointestinal symptoms since infancy and was diagnosed with Crohn's disease at 6 years. He had recurrent sinopulmonary infections and 2 liver abscesses. Two prior DHR assays were reported as normal based on percentage of neutrophils demonstrating oxidative burst (84%, 73%), without reporting NADPH oxidase (NOX) activity measured by mean fluorescence intensity (MFI). Due to high suspicion for chronic granulomatous disease (CGD), a third oxidative burst was obtained from another reference laboratory. It revealed significantly reduced NOX activity in neutrophils. Flow cytometry for NADPH-oxidase specific proteins showed normal expression of gp91phox, p22phox, p67phox and p40phox and absent p47phox. The patient had a heterozygous NCF1 delta GT mutation and a wild-type second allele. He underwent successful hematopoietic stem cell transplantation from a fully matched unrelated donor. DHR assay is the standard diagnostic test for CGD. However, complete interpretation requires both MFI and percentage of positive cells, and variability exists in how DHR is performed and reported by different reference laboratories. This patient's diagnosis and treatment were delayed by a lack of recognition of abnormal test results. It is essential for ordering physicians to understand the test, including performance characteristics, analysis and reporting by laboratories. Further, specific protein flow can be used to confirm an abnormal DHR result enabling rapid genetic triage.