This chapter aims to introduce the reader to the major ethical norms and principles that underpin biomedical research, as well as public health research and practice as they relate to infectious diseases. It outlines some of the key ethical issues highlighted in the literature which are likely to arise when designing and conducting molecular investigations. These include the ethical significance of working with vulnerable individuals and communities; respecting privacy and confidentiality within the context of open science; managing the relationship between molecular research and practice; and the ethical challenges of working across cultures. The chapter goes on to explore practical ethical issues, such as informed consent, data-sharing, research collaborations and conflicts of interest, that researchers and practitioners may encounter and how these may be addressed. Lastly, a brief overview of legal and regulatory frameworks relevant to molecular epidemiology and infectious disease are presented. The chapter aims to equip researchers and practitioners to be able to identify, evaluate and act upon the ethical aspects of the professional practice in molecular epidemiology for infectious disease.