This research investigates the effect of alternative assessment on students’ perception and achievement in six, 9th grade biology classrooms. Students’ perception was determined through the use of a Likert scale questionnaire which compared confidence levels and preference for traditional verses alternative assessment. Achievement was measured according to academic grades from both types of assessment. Our findings indicate a significant student preference for multiple-choice exams as well as greater achievement in traditional assessment methods. The results suggest a further investigation of assessment practices is needed in order to more accurately describe the relationship between assessment strategies, student perception and student achievement.