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Genomic technologies are transforming infectious disease surveillance and control, particularly in resource-limited settings such as Uganda. This review examines ongoing efforts by the Department of National Health Laboratory and Diagnostic Services - Central Public Health Laboratories (NHLDS-CPHL) to integrate genomics into public health strategies. We highlight key advancements, lessons learned, and opportunities, including expanded genomic testing capacity, localized bioinformatics infrastructure, and reinforcement of surveillance systems. Through use-case studies on COVID-19, HIV/AIDS, malaria, Ebola, Mpox, rotavirus, and cholera, we demonstrate the impact of genomics on improving diagnostic accuracy, disease monitoring and outbreak response, identifying drug resistance, and informing targeted public health interventions. Despite these successes, challenges, including but not limited to infrastructure gaps, funding constraints, and ethical considerations, remain, underscoring the need for policy, regulation, and capacity enhancement as well as global collaboration to effectively address these obstacles. Lessons learned from these efforts provide valuable recommendations for optimizing and sustaining genomic programs in low-resource settings. By leveraging genomics, Uganda can further strengthen its ability to detect, monitor, and respond to emerging and re-emerging health threats, ultimately enhancing disease control measures and public health resilience.