Infectious diseases remain a leading cause of global morbidity and mortality, underscoring the need for rapid, accurate, and comprehensive diagnostic approaches. Advances in omics technologies have evolved our ability to detect, characterize, and monitor pathogens. Together, these technologies offer a systems-level perspective that enhances diagnostic accuracy which can be applied both in clinical and public health laboratories, to ameliorate infectious diseases policies and strategies. Despite significant progress, challenges remain in terms of cost, data integration, standardization, and clinical translation. Future directions include the development of multi-omics platforms, real-time sequencing technologies, and robust bioinformatics pipelines to accelerate implementation in routine clinical practice. This review highlights the current landscape, key applications, and future potential of omics-based diagnostics in combating infectious diseases.