Recent education reform efforts advocate teaching the process of science (inquiry) in undergraduate lecture and laboratory classes. To meet this challenge, professional development for the graduate student instructors (teaching assistants, or TAs) often assigned to teach these classes is needed. This study explored the implementation of an observation protocol designed to support peer observation and reflection among TAs teaching inquiry-based undergraduate biology laboratories. The researchers of this study and TA-peers who are experienced in teaching inquiry used the protocol to observe novice TAs at the beginning, mid-point, and end of a semester-long teaching assignment. Novice TAs used a modified version of this protocol to observe an experienced and a novice TA. Analysis of post-semester interview data indicated engaging in both sets of observations and post-observation discussions facilitated by the protocol gave novice TAs new ways to teach content, guidance on implementing pedagogical theory, and means to improve communications with students and classroom management skills. Researchers also used quantitative data collected from the observations to document frequency of teaching and student behaviors associated with teaching inquiry and how these frequencies changed during the semester. Considerations for how to use both sets of data to inform changes in TA professional development are discussed.