In this article, we describe a process of the San Francisco collaboration to select optimal measures of linkage to care in response to the Enhanced Comprehensive HIV Prevention Planning program of the Centers for Disease Control and Prevention and to understand the implications of measure selection and the challenges of accessing data sources to measure outcomes along the HIV care continuum. Challenges identified are the variety of definitions of linkage to care and the nonintegrative nature of the multiple data systems necessary to measure linkage to care and other continuum outcomes. The choice of linkage measures, which at the extremes is a choice between higher-resolution measures based on clinical visit data in a subset of patients vs. a lower-resolution proxy measure based on surveillance data, has key implications. Choosing between the options needs to be informed by the primary use of the measure. For representing trends in the overall performance and response to interventions, more generalizable measures based on surveillance data are optimal. For identifying barriers to linkage to care for specific populations and potential intervention targets within the linkage process, higher-resolution measures of linkage that include clinical, laboratory, and social work visit information are optimal. Cataloging the different data systems along the continuum and observations of challenges of data sharing between the systems highlighted the promise of integrated data management systems that span HIV surveillance and care systems. Such integrated data management systems would have the ability to support detailed investigation and would provide simplified data to match newly developed, cross-agency Health and Human Service measures of HIV care continuum outcomes.