Control measures for H5N1 avian influenza involve increased biosecurity, monitoring, surveillance and vaccination. Subclinical infection in farmed ducks is important for virus persistence. In major duck rearing countries, homologous H5N1 vaccines are being used in ducks, so sero-surveillance using H5- or N1-specific antibody testing cannot identify infected flocks. An alternative is to include a positive marker for vaccination. Testing for an antibody response to the marker would confirm approved vaccine use. Concurrent testing for H5 antibody responses would determine levels adequate for protection or indicate recent infection, with an anamnestic H5 antibody response requiring further virological investigation. In this study, we have evaluated the use of a TT marker in ducks given avian influenza vaccination. Wild or domestic ducks were tested for antibodies against TT and all 463 ducks were negative. High levels of TT-specific antibodies, produced in twice-TT vaccinated Muscovy ducks, persisted out to 19 weeks. There was no interference by inclusion of TT in an inactivated H6N2 vaccine for H6- or TT-seroconversion. Thus TT is a highly suitable exogenous marker for avian influenza vaccination in ducks and allows sero-surveillance in countries using H5N1 vaccination.