Introduction: Disseminated tuberculosis (TB) is due to hematogenous spread of tubercle bacilli. Patients with immunocompromised factors are a high risk for disseminated TB. A patient with renal tuberculosis may be asymptomatic, with the discovery of the disease after severe kidney destruction A few case reports involve immunocompetent patients, particularly healthy adolescents. Herein, we report a very rare case with disseminated tuberculosis in a healthy man, who was revealed to have an idiopathic CD4 lymphocytopenia (ICL). Case description: A previously healthy 35-year-old man presented with a 2-month history of intermittent gross hematuria, dysuria, and weight loss. Urine analysis revealed microscopic hematuria and pyuria. Urine culture was negative for all bacteria. However, Mycobacterium tuberculosis PCR using urine specimens was positive. Enhanced abdominal CT scan were highly suggestive of multiorgan involvement of tuberculosis (kidney, intestine, and lymph node). We diagnosed disseminated tuberculosis and started administering induction therapy with anti-tuberculosis drugs. M. tuberculosis were identified from the urine, sputum, and intestinal tissue after 1 month. He had undergone routine Bacille Calmette-Guerin vaccination and denied a contact history of tuberculosis (TB). The patient was additionally examined for HIV, sex hormone, vitamin D, and immunoglobulin deficiency. Human immunodeficiency virus antigen/antibody test were negative. Testosterone, 25-OH Vitamin D and immunoglobulin level were normal range. However, despite of the patient’s HIV test was negative, he had a low CD4 T cell count. After one year of follow up, we found out that he was not improved CD4 T cell counts. Conclusion: We report a very rare case of disseminated tuberculosis in a healthy young man, who was revealed to have an idiopathic CD4 lymphocytopenia (ICL). Although, our case was not respiratory symptom, and had a small burden of pulmonary tuberculosis, the patient started an initially renal symptom of disseminated tuberculosis.