This study exemplifies how faculty members can develop instruments to assess affective responses of students to the specific features of the courses they teach. Means for assessing three types of affective responses are demonstrated: (a) student attitudes towards courses with differing instructional objectives and methodologies, (b) student self-efficacy (confidence) in completing tasks common to practicing experts, and (c) interests in subject-specific topics and associated intellectual skills. The iterative processes used in refining the instruments and performing the statistical analyses of their effectiveness are detailed. An analysis of data obtained using these instruments is also included. Positive attitudes towards courses emphasizing analytical thinking increased significantly over the course of a 14-week semester, as did the measures of self-efficacy. Despite the rigorous analytical nature of the course experience, the initial strong interest in cell biology topics and higher order thinking skills remained unchanged. There were no significant differences based on gender in any of the affective measures. We discuss the apparent dichotomy, revealed in these assessments, between students' idealistic, academic attitudes towards the course's effectiveness and their opinions of its effects on them personally. We conclude by reporting how insights garnered both from these formal assessments and from anecdotal communications have prompted experimental modifications in the design and conduct of the course. The following are appended: (1) Cellular Biology Self-efficacy (Confidence) Scale; (2) Original, 16-Item Attitude Scale; and (3) Scale Assessing Interest in Cell Biology Topics. (Contains 9 tables and 2 figures.)