Transfers can have an important influence on customer satisfaction and on whether many customers find transit service an attractive option. An empirical investigation of transfers from commuter rail to subway in downtown Boston, Massachusetts, is performed. The research identifies a higher transfer penalty between commuter rail and subway than between subway lines. Fare payment and network familiarity also are shown to affect transfer decisions. Despite a large variation of the transfer experience between the stations analyzed, riders seem to have a similar perception of transfers. For example, in most cases, the perceived transfer penalty has a narrow distribution, with a coefficient of variation below 0.5. Potential applications of the research findings to transit planning are presented.