In this dissertation we examine several issues related to the retention of under-represented minority students in physics and science. In the first section, we show that in calculus-based introductory physics courses, the gender gap on the FCI is diminished through the use of interactive techniques, but in lower-level introductory courses, the gap persists, similar to reports published at other institutions. We find that under-represented racial minorities perform similar to their peers with comparable academic preparation on conceptual surveys, but their average exam grades and course grades are lower. We also examine student persistence in science majors; finding a significant relationship between pedagogy in an introductory physics course and persistence in science. In the second section, we look at student end-of-semester evaluations and find that female students rate interactive teaching methods a full point lower than their male peers. Looking more deeply at student interview data, we find that female students report more social issues related to the discussions in class and both male and female students cite feeling pressure to obtain the correct answer to clicker questions. Finally, we take a look an often-cited claim for gender differences in STEM participation: cognitive differences explain achievement differences in physics. We examine specifically the role of mental rotations in physics achievement and problem-solving, viewing mental rotations as a tool that students can use on physics problems. We first look at student survey results for lower-level introductory students, finding a low, but significant correlation between performance on a mental rotations test and performance in introductory physics courses. In contrast, we did not find a significant relationship for students in the upper-level introductory course. We also examine student problem-solving interviews to investigate the role of mental rotations on introductory problems. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]