Background: Histology laboratory courses are morphologic study in the structure of the cells, tissues, and organs of the body that are mainly examined with a microscope. There are two types of examinations to assess learning outcomes in Taiwan. The first is a traditional practical-based identification for microscopic image (PBIMI) examination, and the second is Microsoft PowerPoint (MS PPT) examination. Whether these two types of examinations exhibit different influences on students’ learning motivation has not been evaluated. Methods: In this study, we compared the grades of dental students and medical students in the National Defense Medical Center who completed PBIMI or MS PPT examinations and investigated the influence of the type of examination on the students’ learning outcomes and motivation. We also conducted a survey among the medical students to confirm the hypothesis concluded from the grade analysis. Results: There was a significant decrease in the percentage of students scoring 61 to 80 in the MS PPT group compared to that in the PBIMI group in the midterm examination of dental students. The average score on the MS PPT examination was significantly higher than that on the PBIMI examination among medical students who completing both examinations. The average failing scores on the midterm examination among the students tested with the PBIMI examination were significantly lower than the scores among the students tested with the MS PPT examination. The results of the survey also showed that the MS PPT examination is easier for students and that they will spend less time learning the material when the MS PPT examination is utilized for assessment. Conclusion: This study suggests that the type of examination affects learning motivation in less self-demanding students. The MS PPT test is easier for the students and leads to less time spent studying for the histology laboratory course, especially among the students with fewer self-demands or less interest in the course.