Heparin-induced thrombocytopenia (HIT) syndrome is a catastrophic complication of heparin therapy that may result in arterial/venous thromboembolic events. The pathophysiology of HIT is mediated by the generation of a functionally and molecularly heterogeneous group of anti-heparin-platelet factor 4 (AHPF4) antibodies that cause platelet/endothelial cell activation/destruction. These AHPF4 antibodies may be of various subtypes and cause differential pathogenic responses during HIT. This study evaluated the differential prevalence and functionality of AHPF4 Ig subtypes (IgA, IgG, and IgM) in plasma samples obtained from clinically suspected HIT patients (n = 111) and two clinical trials. In these trials, a low-molecular-weight heparin, clivarin and unfractionated heparin (UFH) were used to treat deep-vein thrombosis (CORTES) and for prophylaxis of the orthopedic surgery (ECHOS). In the CORTES study, three randomized groups of patients (n = 312-328) received prophylactic treatment with either UFH or clivarin (o.d. or b.i.d.). In the ECHOS study, there were approximately 600 patients per group. Citrated plasma samples were analyzed for cumulative IgA/IgG/IgM and individual Ig subtypes of AHPF4 utilizing ELISA. Functionality of the ELISA-positive samples was ascertained by 14C-serotonin release assay. In clinically confirmed HIT patients (and UFH-treated CORTES and ECHOS samples), the Ig subtyping revealed a predominance of IgG AHPF4 antibodies in contrast to the asymptomatic high AHPF4 antibody titers, which were found to be mostly IgM and/or IgA subtypes. In the clivarin-treated patients in both trials, the prevalence of AHPF4 antibodies was found to be lower (2-3 fold, p < 0.01) in comparison to UFH group. In addition, the clivarin-treated patients with positive AHPF4 antibodies were found to be predominantly of the non-functional type and were found in the order of IgM > IgA > IgG Together, these observations demonstrate that ELISA-detectable IgG subtype in UFH-treated patients may be more likely to cause functional/pathologic responses during HIT syndrome. Thus, determination of IgG subtype of AHPF4 antibodies during HIT syndrome may be crucial in the diagnosis; however, the relevance of the pathologically non-functional (IgA and/or IgM) antibodies and the overall mechanism(s) of these HIT-associatied antibodies need further investigation.