Absence of the inferior vena cava is a rare vascular anomaly, which usually remains asymptomatic in childhood. It is recognized as the risk factor for deep venous thrombosis, since the collateral circulation does not provide adequate drainage of the lower limbs. Mycoplasma pneumoniae is a common cause of community-acquired pneumonia in school-aged children and adolescents. Mycoplasma pneumoniae infection might be associated with deep venous thrombosis but its pathophysiology remains unknown. According to previous reports, deep venous thrombosis due to Mycoplasma pneumoniae infection is associated with positive serum anticardiolipin antibodies. To our knowledge, we describe the first case of deep venous thrombosis associated with Mycoplasma pneumoniae serum antibodies indicating early stage of infection with negative anticardiolipin serum antibodies in adolescent with absence of inferior vena cava. 14-year old boy was admitted to the pediatric unit few days after the appendectomy complaining with pain of the left hip that caused him unable to walk. The pain was accompanied with subfebrile temperature. After clinical examination and additional tests, the boy was diagnosed with a deep venous thrombosis. Computed tomography revealed absence of the vena cava inferior distally to the hepatic veins and varices of the collateral circulation in the pelvis. Anticardiolipin IgM and IgG antibodies and antinuclear antibodies were not detected. Additionally, the Mycoplasma pneumoniae antibodies in classes IgM, IgA and IgG were detected in serum as another risk factor of thrombosis. After the initial treatment with low-molecular-weight heparin in combination with clarithromycin the clinical condition of the patient improved. The patient became a candidate for life-long anticoagulation therapy. In this case Mycoplasma pneumoniae antibodies were associated with deep venous thrombosis in child with congenital absence of inferior vena cava. Uncommonly for deep venous thrombosis due to Mycoplasma pneumoniae infection, anticardiolipin antibodies were not detected in serum. It is important to remember in clinical practice that Mycoplasma pneumoniae affects coagulability and may trigger thrombosis, especially in the presence of other risk factors. The pathophysiology of this process remains unknown.