Introduction: Pneumococcal conjugate vaccines are expensive relative to those in the EPI systems of low-income countries. The current single-dose presentation costs more to store in the cold chain relative to multi-dose presentations but also has lower wastage rates. It is, therefore, important to determine the optimal balance of vial size and storage costs after adjusting for wastage. Objectives: To project the cost implications of wastage when vaccine wastage rates vary across vial sizes using country specific wastage data. Results: Only 19 (26%) of 72 GAVI eligible countries had analyzable wastage data at WHO/HQ. The median wastage rates for single, 2- and 10-dose vials were 5%, 7% and 10% respectively. However wastage varied between 1%-10%, 1%-27% and 4%-44% for single, 2- and 10-dose vials respectively. The increased variance for multi-dose vial wastage implied wastage costs potentially greater than the savings realized from lower storage volumes. Methods: For each potential vial size, we estimated cold chain costs and the cost of wasted vaccine doses using country level wastage data and projections of the price per dose of vaccine and cold chain storage. Conclusions: The optimal vial-size for PCV is dependent upon country specific wastage rates but few countries have these data. There may be a role for both single and multi-dose vials that is best determined by local management and storage capacities making local wastage data critical. Without effective wastage monitoring and control there is a risk that wastage costs will possibly exceed the savings from multi-dose vials' lower storage costs.