Deep learning has revolutionized biomedical research by providing sophisticated methods to handle complex, high-dimensional data. Multimodal deep learning (MDL) further enhances this capability by integrating diverse data types such as imaging, textual data, and genetic information, leading to more robust and accurate predictive models. In MDL, differently from early and late fusion methods, intermediate fusion stands out for its ability to effectively combine modality-specific features during the learning process. This systematic review comprehensively analyzes and formalizes current intermediate fusion methods in biomedical applications, highlighting their effectiveness in improving predictive performance and capturing complex inter-modal relationships. We investigate the techniques employed, the challenges faced, and potential future directions for advancing intermediate fusion methods. Additionally, we introduce a novel structured notation that standardizes intermediate fusion architectures, enhancing understanding and facilitating implementation across various domains. Our findings provide actionable insights and practical guidelines intended to support researchers, healthcare professionals, and the broader deep learning community in developing more sophisticated and insightful multimodal models. Through this review, we aim to provide a foundational framework for future research and practical applications in the dynamic field of MDL.