公用儀器室設立目的在於提供貴重儀器設備與特殊技術服務，以協助本所研究進行。目前公用儀器室設有五個核心設施：
- 光學顯微鏡設施：雷射共軛焦顯微鏡包括Ziess 510Meta，Ziess 700，Ziess 700 stage以及Ziess 780；傳統螢光顯微鏡系統包括Ziess Axiovert 200M，Leica DMI6000B；高通量細胞螢光分析系統MD-ImageXpress Micro Imaging XL System。提供多種顯微鏡相關應用，包括活細胞長時間觀察；高解析共焦影像擷取；快速螢光影像擷取；FRET；3D影像重組；大量細胞統計；高解析大面積拼圖等應用。
- 核酸定序設施：此設施由院內儀器服務處設置於生醫所，為全院同仁提供核酸定序服務。使用之定序儀為Applied Biosystems 3730xl DNA Analyzer。
- 流式細胞分析分選設施：設施內設置多台流式細胞儀，其中流式細胞分析儀為使用者自行預約上機操作。流式細胞分選儀則為專人操作，此設施由院內儀器服務處設置於生醫所，為全院同仁提供細胞分選服務。核心設施並提供儀器操作與分析軟體的教育訓練及相關實驗諮詢。
- 蛋白質體核心設施：此設施提供多種服務項目，包含蛋白質定性分析及相對表現定量分析。定性分析包含蛋白質分子量測定、蛋白質身份鑑定、轉譯後修飾點鑑定。定量分析，提供標記(labeled)及免標記(label-free)等多種相對表現定量法。此外，也提供多項樣品前處理之訓練課程。
- 化學合成設施：提供小分子藥物合成服務。
The IBMS has five core facilities that provide instrument and technical support for IBMS researchers.
- Confocal Microscopy Core Facility. It houses five confocal microscopes (Ziess 510 Meta, Ziess 700, Ziess 700 stage, Ziess 780) and two fluorescence microscopes (Ziess Axiovert 200M and Leica DMI6000B) for confocal microscopy and live imaging studies.
- DNA Sequencing Core Facility. It uses the ABI 3730 xl DNA Sequencer to determine DNA sequences. The service is open to researchers in IBMS as well as Academic Sinica.
- Proteomics Core Facility. It provides services for protein identification (protein ID), post-translational modifications (PTMs) of proteins, and large scale protein quantitation.
- Flow Cytometry Core Facility. It provides flow cytometric analysis and cell sorting services as well as flow cytometry training courses. The flow cytometry analysis is operated by the users. The cell sorting service is operated by a skillful research assistant and is open to IBMS as well as Academia Sinica researchers.
- Chemical Synthesis Lab. It provides the service for the synthesis of small molecule drugs.