The principles of plant physiology are best learned in an environment where students are directly engaged in the process of scientific inquiry. Working from this assumption, we have developed a two-stage approach to laboratory instruction that fosters student-directed research within an undergraduate plant physiology course. During the first 10 weeks of a 16-week semester, students develop competency in measuring physiological variables by using an array of standard analytical techniques. A core set of 10 laboratory experiments provides structured instruction and teaches the principles of modern physiological analyses. During week 11, students observe a demonstration of a plant response, where the underlying cause of the phenomenon is not evident. Working together in groups of three or four, students hypothesize on the physiological mechanisms that may be involved. After submitting a statement of hypothesis and a plan of study, each group then requests the necessary instrumentation, plant material and greenhouse and/or growth chamber space to conduct their experiments. Results of their experimentation are presented during week 15 in both written and oral formats. The approach appears to help students to integrate and connect learnings from earlier in the semester to solve a defined problem. Further, students learn how to judge the reliability of experimental results and to evaluate whether conclusions drawn are justified by the data.