The discussion forum is a significant component of online courses. Instructors and students rely on these asynchronous forums to engage one another in ways that potentially promote critical thinking, meaningful problem solving, and knowledge construction. In spite of the importance of these forums, predominantly used methods for assessing the content and outcomes of these forums has often been limited to frequency counts and other quantitative measures. Only recently have researchers developed protocols for conducting meaningful qualitative analysis of online discussion forums. This study compares the application of two content analysis protocols for online discussion boards by applying both to the content of a one-week student-led discussion. Our analysis provides a detailed description of how to use both protocols and evaluates each for its strengths and weaknesses toward the overall goal of providing educators and researchers with valid tools for assessing discussion forum content.