Uncertainty in product development and market demand can affect facility design and construction. Adding flexibility in manufacturing processes can mitigate this uncertainty, but can also create costly solutions. This is particularly true when manufacturing facilities have long design and construction lead times. In these cases, manufacturers take risks by starting facility construction before the product development is complete to meet time-to-market needs. Similarly, uncertain market demand can create the need to build facilities with additional volume or the ability to expand. This paper presents an analysis of how manufacturing flexibility affects building system costs and proposes a solution for understanding the trade-offs. The research method maps various types of manufacturing flexibility (e.g., process, routing, volume, etc.) to ASTM UNIFORMAT II building systems (e.g., substructures, shell, interiors, etc.). Based upon this mapping, initial cost models are proposed to explore the relationship between manufacturing flexibility and facility construction cost. The models are intended for use in the earliest stages of capital facility planning. These results will help manufacturing facility owners, designers, and constructors make informed decisions about how to build flexibility into their buildings at lower costs while mitigating for uncertainty and meeting time-to-market needs.