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Background Laboratory quantification of IgG subclasses (IgGSc) is a well-established second-line tool for differential diagnosis of immune deficiencies. However, so far there is still no internationally approved standard available for IgGSc, and different assays are prone to produce divergent results. In this study, we evaluated the comparability and equivalence of two commercially available IgGSc assays, one being the Siemens IgGSc assay on a BN ProSpec analyzer and the other being The Binding Site (TBS) IgGSc assay on a Roche cobas c502 analyzer. Methods We analyzed a total of 50 patient plasma samples obtained over a 3-month period with both IgGSc assays and compared the resulting data based and the CLSI EP09-A3 method comparison guideline. Results Depending on the analyzed IgGSc type, the average relative differences in IgGSc concentration (g/L) between the two assays were considerable, starting with −13.5% for IgG1 and 11.3% for IgG2, over −47.3% for IgG4, and up to 52.9% for IgG3. Applying the assay-specific reference intervals, the classification agreement (below, within, or above the reference range) ranged from 88% to 90% for the individual subclasses. However, only 68% of samples showed an overall classification agreement. Conclusion The comparability of the two IgGSc assays proved to be limited and might be considered similar at best on the diagnostic level. Laboratory specialists as well as clinicians therefore should be cautious when using and interpreting IgGSc measurements obtained with different assays or analyzers.