This study used a Hierarchical Linear Modeling (HLM) approach to investigate relationships between student motivation, higher-order thinking skills, quality of teaching and learning, teacher student relations, student satisfaction with course contribution to their learning, and active learning strategies, with a sample of 2,190 undergraduate students. The HLM results indicate significant differences among departments in student motivation (2 (31) = 260.90, p less than 0.000). This variation among university departments suggests that the department-level variables might have accounted for the differences in motivation scores. An Intra-class correlation for this sample is 0.17, indicating that 17% of variance in motivation was among departments. Further, the reliability of the sample mean in any department for the true mean department motivation was 0.82. All three level-1 variables were found to vary among departments. Cross-level interactions showed that main effect of quality of teaching and learning was significant while student satisfaction with course did not provide significant contribution to their learning or to the explanation of the variation in motivation. The slopes for active learning strategies, higher-order thinking skills, and teacher student relations were all positive and significant. (Contains 6 tables.)