A number of important health policy issues, such as the allocation of flu vaccines during a pandemic, require society to determine priorities across different age groups. Cost-effectiveness analysis (CEA) and related methods of economic evaluation are often useful for determining optimal resource allocations. Using the examples of recently evaluated vaccine interventions, we show that current methods of CEA are likely to under-value health interventions for young people, relative to societal preferences inferred from research on age preferences and the value of health over time. These findings demonstrate important considerations regarding how society distributes health resources across age groups.