Transit riders negatively perceive transfers because of their inconvenience, often referred to as a transfer penalty. Understanding what affects the transfer penalty can have significant implications for a transit authority and also lead to potential improvements in ridership forecasting models. A new method was developed to assess the transfer penalty on the basis of onboard survey data, a partial path choice model, and geographic information system techniques. This approach was applied to the Massachusetts Bay Transportation Authority subway system in downtown Boston. The new method improves the estimates of the transfer penalty, reduces the complexity of data processing, and improves the overall understanding of the perception of transfers.