Objective The presence of deep venous thrombosis (DVT) in a cryptogenic stroke (CS) patient with a right-to-left shunt (RLS) may lead to the development of paradoxical embolism. The aim of the present was to investigate the prevalence of DVT and pulmonary embolism (PE) in CS patients and the clinical features of CS in relation to DVT location and the presence of PE. Methods The medical records of 903 patients with cerebral infarction were retrospectively reviewed. For patients with a diagnosis of CS, contrast saline transcranial color-coded sonography was performed to identify an RLS. DVT and PE were assessed by duplex ultrasonography and/or contrast-enhanced computed tomography. Proximal DVT (P-DVT) was defined as DVT in the popliteal, femoral, or iliac veins, and distal DVT (D-DVT) was defined as DVT at other locations. The patients were divided into three groups: CS with P-DVT and/or PE (P-DVT/PE) group; CS with D-DVT (D-DVT) group; and CS without DVT (no DVT) group. Results Seventy-two (37%) of 194 patients with CS had an RLS. The median time to first DVT examination from stroke onset was three days. Twenty-nine percent of CS patients with an RLS had DVT. The P-DVT/PE group comprised 8.3% of the CS patients with an RLS and included a larger number of patients with multi-territory infarction than the D-DVT group. The D-DVT and P-DVT/PE groups tended to be female and older, while the P-DVT/PE group tended to have pre-stroke disability. Conclusion CS patients, especially those with multi-territory lesions, should be immediately examined for DVT and PE.