A 42-year-old Japanese woman was admitted for the evaluation of proteinuria. She had a history of four habitual abortions and valvular heart disease, including severe mitral regurgitation and moderate tricuspid regurgitation. A kidney biopsy showed fibrointimal thickening of interlobular arteries, fibrin thrombosis, and associated focal segmental sclerosis. Although the standard test for antiphospholipid (aPL) antibodies was negative, the patient was diagnosed with antiphospholipid syndrome (APS)-related disease by testing for phosphatidylserine dependent anti-prothrombin anticardiolipin antibody, a non-criterial aPL antibody. A kidney biopsy may lead to a diagnosis of APS in patients with negative laboratory test findings for APS.