Hepatitis A virus (HAV) and hepatitis E virus (HEV) infections are endemic in most developing countries, including Nepal and Afghanistan, and may cause outbreaks in military personnel. Previously, more than 99% of new British Gurkha recruits were already immune to HAV because of prior infection, but this may be declining due to improved living conditions in their countries of origin. Acute HAV infections have occurred in Gurkha soldiers serving in Afghanistan, which made them unfit for duty for 2–3 months. In one case, early serological diagnosis was impeded by IgM results against both HAV and HEV that were caused by cross-reactivity or persistence from a previous infection. These cases have led to a policy change whereby all Gurkha recruits are now tested for previous HAV infection and if negative they are offered vaccination. Meanwhile, HEV infection remains a significant threat in Nepal and Afghanistan with low levels of background immunity and no commercially available vaccine.