Abstract Neoplastic progression is a process of somatic evolution, yet few evolutionary tools have been adapted to measure the dynamics of progression. We have recently shown that traditional analyses of cross-sectional sampling of neoplasms usually infers the wrong order of events in progression. In contrast, phylogenetic methods applied to multiple samples within a neoplasm can accurately infer the order of events. Furthermore, longitudinal sampling can be used to estimate mutation rates, including chromosomal aberration rates, using phylogenetic methods developed to study viral evolution in vivo. We have applied these tools to study the dynamics of progression in Barrett's esophagus and the effects of non-steroidal anti-inflammatory drugs on that somatic evolution. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr IA15.