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Organic chemistry is a class well known to be difficult and necessary for many careers in the sciences, and as a result, has garnered interest in researching ways to improve student learning and comprehension. One potential way involves using eye tracking techniques to understand how students visually examine questions. Organic chemistry involves many unique visual tools, both in two- and three-dimensions, to convey meaning regarding chemical structure and transformation. Developing tools for better learning about and understanding how students approach these problems could provide educators with a greater ability to improve their classroom presentations and educational techniques. A methodology for using eye tracking technology to improve organic chemistry education was developed through a new process of question design, implementation, and data analysis on large samples of students. This process involved designing multiple-choice organic chemistry questions suitable for eye tracking technology to probe student comprehension of a variety of specific topics. This led to the development of a methodology for future implementation while providing useful information on how students approach topics such as orbital hybridization, acid base reactions, chemical structures, isomeric relationships, and alkene reactions. Eye tracking technology has been underutilized regarding these topics, resulting in new insights being gleaned using these questions, while simultaneously improving the developing methodology. This method begins by building on previous novel question development, using that research to guide the question design at the beginning of the project. These questions were then formatted to fit the eye tracking technology available, specifically allowing for the formation of areas of interest (AOIs) wherein eye tracking data was gathered. These questions were then asked to undergraduate organic chemistry students at the University of Georgia and scheduled at times corresponding to when students had recently studied the relevant material. The data was then calculated and reported in the form of fixation counts, average fixation duration, and total fixation duration for each AOI in each question, and statistical analyses were conducted using a Welch Two Sample t test to compare the averages for these variables across two groups: students who answered correctly and those who answered incorrectly. [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.]