The United States produces too few Science, Technology, Engineering, and Mathematics (STEM) graduates to meet demand. We investigated scientific reasoning ability as a possible factor in STEM retention. To do this, we classified students in introductory biology courses at a large private university as either declared STEM or non-STEM majors and assessed their reasoning ability using the Lawson Classroom Test of Scientific Reasoning. We then obtained their declared majors 1 to 4 years later. We found that reasoning ability correlates with high-level performance and final course grades. In addition, results indicate that STEM majors have higher reasoning skills than non-STEM majors but not until after the freshman year. However, we show that reasoning ability does not predict retention or declaration of a STEM degree and suggests instead that increased reasoning skills are a product of learning. We suggest educational interventions that may plug the leaky pipeline in STEM education.