Metacognition is a valuable tool for learning, since it is closely related to self-regulation and awareness of one's own affect. However, methods for automatically detecting and studying metacognition are scarce. Thus, in this paper we describe an algorithm for automatic detection of metacognitive language in writing. We analyzed text from the forums of two online, university-level science courses, which revealed common patterns of phrases that we used for automatic metacognition detection. The algorithm we developed exhibited high accuracy on expert-labeled metacognitive phrases (Spearman's rho = 0.878 and Cohen's kappa = 0.792), and provides a reliable, fast method for automatically annotating text corpora that are too large for manual annotation. We applied this algorithm to analyze relationships between students' metacognitive language and their academic performance, finding small correlations with course grade and medium-sized differences in metacognition across courses. We discuss how our algorithm can be used to advance metacognitive studies and online educational systems.