Objective The purpose of this article was to identify some common organizational features of multisector health care alliances (MHCAs) and the analytic challenges presented by those characteristics in assessing organizational change. Data Sources Two rounds of an Internet-based survey of participants in 14 MHCAs. Study Design We highlight three analytic challenges that can arise when quantitatively studying the organizational characteristics of MHCAs - assessing change in MHCA organization, assessment of construct reliability, and aggregation of individual responses to reflect organizational characteristics. We illustrate these issues using a leadership effectiveness scale (12 items) validated in previous research and data from 14 MHCAs participating in the Robert Wood Johnson Foundation's Aligning Forces for Quality (AF4Q) program. Findings High levels of instability and turnover in MHCA membership create challenges in using survey data to study changes in key organizational characteristics of MHCAs. We offer several recommendations to diagnose the source and extent of these problems.