Title: MSQ-BioBERT: Ambiguity Resolution to Enhance BioBERT Medical Question-Answering. Abstract: Bidirectional Encoder Representations from Transformers (BERT) and its biomedical variation (BioBERT) achieve impressive results on the SQuAD or medical question-answering (QA) datasets, and so they are widely used for a variety of passage-based QA tasks. However, their performances rapidly deteriorate when encountering passage and context ambiguities. This issue is prevalent and unavoidable in many fields, notably the medical field. To address this issue, we introduce a novel approach called the Multiple Synonymous Questions BioBERT (MSQ-BioBERT), which integrates question augmentation, rather than the typical single question used by traditional BioBERT, to elevate performance. Experiments with both an ambiguous medical dataset and open biomedical datasets demonstrate the significant performance gains of the MSQ-BioBERT approach, showcasing a new method for addressing ambiguity in QA tasks. 