In this study, we analyzed the usefulness and limitations of MLPA in antithrombin deficiency, focusing on the search for potential SVs that might be obscured by the current algorithm designed to characterize the molecular basis of this severe thrombophilia, which restricts the analysis of potential SVs by MLPA only to cases with type I deficiency and no pathogenic genetic variants identified by the sequencing of SERPINC1. The gene discussed is SERPINC1; the disease is Rare hereditary thrombophilia.