Student motivation in medical education courses is essential for the development of life-long medical knowledge. Researchers have demonstrated that student learning in anatomy courses, fundamental to students' future medical learning, has suboptimal long-term outcomes. The purpose of this study was to investigate how medical students' motivation-related perceptions and course effort were different during the academic year through varied course content and elements of instruction. The study was guided by the MUSIC Model of Motivation theoretical framework and nested in the pragmatic paradigm. First-year medical students enrolled at a small, public allopathic medical school in the southeastern United States were surveyed and interviewed regarding their course perceptions. Quantitative data from 18 students and qualitative data from 14 students indicated that students' motivation-related perceptions and effort do vary over different course content and elements of instruction. Students consistently reported lower motivation-related perceptions and effort for prerecorded lectures, whereas they reported more positive motivation-related perceptions and effort for cadaver dissection. Results also indicated variability in motivation-related perceptions and effort among specific block content areas (e.g., musculoskeletal, cardiovascular, abdominopelvic). Study findings resulted in a variety of suggestions for course instructors on how anatomy course design and instructional practices could be intentionally adjusted in the interest of fostering student motivation and engagement. Implications for course design and instruction included general course guidance (e.g., clinical relevance, clear and broad understanding of course usefulness), prerecorded lecture recommendations (e.g., catalogued for easy reference, short and focused, effective use of visual and verbal elements), and cadaver lab instruction guidance (e.g., faculty and upper-level student engagement, student preparation expectations). / Doctor of Philosophy / The purpose of this study was to investigate how medical students' motivation-related perceptions and course effort were different during the academic year through varied course content and elements of instruction. The study was guided by the MUSIC Model of Motivation which is a resource course instructors can use to develop their courses in ways that support students' motivation and engagement. The MUSIC Model is an acronym (i.e., eMpowerment, Usefulness, Success, Interest, and Caring) and each letter represents one of five categories of strategies that teachers can use to motivate students. Instructors who use strategies in these categories can improve student motivation which can help encourage students to engage in their learning. First-year medical students enrolled in an anatomy course at a small, public medical school in the southeastern United States were surveyed and interviewed regarding their perceptions of the anatomy course. Information gathered from this study indicated that students' motivation and engagement vary over different course content and elements of instruction. Students consistently reported lower motivation-related perceptions and effort for prerecorded lectures. Students reported more positive motivation-related perceptions and effort for cadaver dissection. Results also indicated unevenness in motivation-related perceptions and effort among specific block content areas (e.g., musculoskeletal, cardiovascular, abdominopelvic). This study offered a variety of suggestions for course instructors on how anatomy course design and instructional practices could be intentionally adjusted in the interest of fostering student motivation and engagement.