Several highly specific gene mutations have been discovered in malignant lymphoma. Mutations of the MYD88 gene have been detected in lymphoplasmacytic lymphoma and in some cases of diffuse large B-cell lymphoma. We report here a case in which detection of such mutation led to a definitive diagnosis. A 76-year-old woman developed a fever of unknown origin. Physical findings revealed no evident signs of infection or lymphadenopathy. Although serum sIL-2R levels were high, computed tomography revealed only mild hepatosplenomegaly with no lesions from which a biopsy could be taken. We performed a bone marrow examination, which initially did not lead to a diagnosis. However, due to progressive worsening of the patient’s systemic condition and noted increased splenomegaly on computed tomography, we performed genetic testing which included the above. This testing detected mutation of the MYD88 gene in bone marrow cells. We strongly suspected malignant lymphoma and conducted further detailed examination, which led to the diagnosis of intravascular large B-cell lymphoma. Genetic testing may be an extremely useful method that can serve as a decisive factor in diagnosing malignant lymphoma that is otherwise difficult to diagnose.