This paper describes an innovative method to evaluate students' learning after teaching the topic of stereochemistry using molecular models in an organic chemistry course for second-year pharmacy students at Princess Nourah bint Abdulrahman University. This method is practical and relevant and directly measures the intended learning skills. It is also easy to structure, standardized, and less time-consuming to grade. The students' outcomes using this method are presented and compared to outcomes of a conventional assessment method using a two-dimensional (2D) paper-based exam.