This article examines health target-setting in 12 former Soviet countries: Armenia, Azerbaijan, Belarus, Georgia, Kazakhstan, Kyrgyzstan, Moldova, Russia, Tajikistan, Turkmenistan, Ukraine, and Uzbekistan. We explored which health targets were set out in national health strategies and within the context of the United Nations initiative on the Millennium Development Goals (MDGs). We found that few former Soviet countries embraced health targets in national health strategies that were quantitative and time-bound. In contrast, measurable and time-bound targets were adopted by almost all countries in the region within the MDG initiative. As the MDG initiative failed to reflect the considerable burden of non-communicable disease in the region, and focussed entirely on communicable disease and mother and child health, this meant that health targets were missing for one of the most severe health challenges in the former Soviet countries. The quality of health data that could guide national health policies is another major challenge for the control of both communicable and non-communicable disease, as well as improvements in mother and child health.