Immunoglobulin A (IgA) nephropathy is the most common glomerular disease, and it often manifests as persistent microscopic hematuria or gross hematuria. Fabry disease and Alport syndrome are hereditary diseases caused by mutation of genes, and these diseases are rare in China. At present, patients can be diagnosed with IgA nephropathy by clinical manifestations and laboratory examinations, but there is still controversy about the simultaneous diagnosis of Alport syndrome and Fabry disease in patients with IgA nephropathy. The present case was a 17-year-old girl with hematuria and proteinuria who underwent a renal biopsy. Light microscopy and immunofluorescence showed that IgA was deposited in the mesangium. Under electron microscopy, zebra bodies with a lamellated structure were detected. A gene test showed a COL4A3 gene mutation. The patient was administered prednisone 40 mg once a day and dispersible tablets of mycophenolate mofetil 0.75 g two times a day. The patient’s condition showed a trend of remission. The findings in our case emphasize the importance of renal biopsy and gene detection in hereditary kidney disease, especially for Fabry disease and its rare coexistence with Alport syndrome.