The experiences of middle school science teachers at two schools in the southeastern US who participated in collaborative, sustained, whole-school professional development and their implementation of standards-based instructional practices are the focus of this study. Participants were involved in their second year of the professional development experience. The research question that was explored was "How are science teachers implementing standards-based instruction while participating in effective professional development experiences?" Data collected in the form of teacher interviews and classroom observations using an observation protocol. Findings indicate that even with effective professional development, teachers implement standards-based instructional practices at varying levels. The reasons for these differences are discussed and the role of teacher beliefs and the impact of beliefs, experience and support from administrators on professional development efforts are discussed. Implications for future science education reform stakeholders and professional development efforts are revealed.