Obesity has increased at an alarming rate across the world and, in turn, rates of non-communicable diseases have escalated. In Eastern Europe, this epidemic has probably occurred at a later stage than the West due to the economic transition following the demise of communism. Knowing how these trends will change is important. We used a micro-simulation model to project obesity trends and related incidence of coronary heart disease and stroke, cancer and type 2 diabetes 20 and 40 years into the future. Where nationally representative data were available, obesity levels were shown to increase with most prominent increases seen amongst men in Latvia and Estonia, and amongst women in Croatia and Latvia. The exception was Lithuania where a decrease in overweight and obesity was observed in both men and women. We showed that interventions effective in reducing obesity would have a significant impact upon the number of new cases of each disease. It is necessary to improve surveillance of obesity and disease incidence as well as implement policies that are effective in reducing body fat.