Recent education reforms including the "Next Generation Science Standards" emphasize integrating engineering into K-12 science instruction. Although prior studies have characterized engineering design (ED) in K-12 settings, no validated protocols attempt to characterize ED integration in secondary science classrooms. The present study used the ED and observation protocol literature to develop, validate, and test the reliability of the Classroom Observation Protocol for Engineering Design (COPED) instrument. Consistent with the ED literature, the COPED characterizes two components of ED: process and habits of mind. To use COPED, researchers code for ED process components, engineering habits of mind, and instructional grouping in 2-min increments. Researchers also record qualitative field notes. Post-observation, researchers include descriptions of disciplinary ties and ED structure. Support for content validity was established through two cycles of expert panel review and revision. Interrater reliability for the instrument was Cohen's K = 0.81. The data collected from the reliability study were subsequently analyzed to demonstrate the utility of COPED in characterizing ED integration. The COPED provides researchers a tool to systematically characterize ED instruction within secondary science classrooms. Using COPED to characterize ED may support science educators in developing ED-related teacher preparation and professional development.