Instructors and the teaching practices they employ play a critical role in improving student learning in college science, technology, engineering, and mathematics (STEM) courses. Consequently, there is increasing interest in collecting information on the range and frequency of teaching practices at department-wide and institution-wide scales. To help facilitate this process, we present a new classroom observation protocol known as the Classroom Observation Protocol for Undergraduate STEM or COPUS. This protocol allows STEM faculty, after a short 1.5-hour training period, to reliably characterize how faculty and students are spending their time in the classroom. We present the protocol, discuss how it differs from existing classroom observation protocols, and describe the process by which it was developed and validated. We also discuss how the observation data can be used to guide individual and institutional change.