To date, risk profiles based on the known common susceptibility variants have limited value in predicting risk of disease but they could be used for risk stratification in prevention programmes at population level. We illustrate the potential utility of polygenic risk stratification using the case of population-based screening for prostate and breast cancer. We compared the number of individuals eligible for screening and the number of cases potentially detectable by screening in a population undergoing screening based on age alone with a population undergoing stratified screening based on age and polygenic risk profile. Stratified screening strategy based on age and genetic risk would potentially improve the efficiency of screening programmes and reduce their adverse consequences. Organisational, ethical, legal and social issues need to be addressed before stratified screening programmes could be implemented.