•Thrombosis and thrombocytopenia after SARS-CoV-2 viral vector vaccine suggests vaccine-induced immune thrombotic thrombocytopenia (VITT).•Thrombosis in unusual sites (splenic, portal, mesenteric, adrenal) is typical of VITT.•Anti-PF4 antibody tests, if available, should be undertaken rapidly for diagnosis.•Intravenous immunoglobulin (IVIg) could mask functional tests to confirm a diagnosis of VITT.•Treatment with IVIg may be associated with false-negative functional tests. Vaccine-induced immune thrombotic thrombocytopenia (VITT) has emerged as a rare side effect of adenoviral vector-based vaccines against coronavirus disease 2019 (COVID-19), and is most frequently reported after use of the Vaxzevria (AstraZeneca) vaccine. This report describes a case of severe thrombocytopenia associated with massive pulmonary embolism and portal vein thrombosis occurring 13 days after the administration of the single-dose adenoviral vector-based vaccine Ad26.COV2.S (Janssen Vaccines). Based on early clinical suspicion, the patient quickly received treatment with corticosteroids and intravenous immunoglobulin, followed by a rapid increase in platelet count that allowed timely administration of full-dose anticoagulation. Treatment with intravenous immunoglobulin, however, could mask the ability of anti-platelet factor 4-heparin antibodies to bind and activate platelets in the presence of heparin, leading to false-negative results on the immunoassay functional test. Therefore, if VITT is suspected, blood samples for diagnostic confirmation should be collected prior to any treatment to improve diagnostic performance.