Abstract In mammals, the profoundly different pathways of male and female sex development are decided by a genetic coin toss; at fertilization either an X or Y chromosome is inherited from the father to unite with the X chromosome, which is always inherited from the mother. These differences begin to unfold during fetal development, when the TDY (Testis determining factor on Y chromosome) is activated in males and acts as a switch that diverts the fate of the undifferentiated gonadal primordia, the genital ridges, towards testis development. If this does not occur, alternative molecular cascades drive the genital ridges toward ovary development. In this paper, we present data obtained from conducting a series of experiments using the mouse model, designed to review the differences between male and female gonads at the molecular and histological levels. This project-based approach is intended for an undergraduate 14-week course (laboratory component of Developmental Biology) at American University in Cairo. Over the course of the semester, we examined the differential expression of Zfy (zinc finger Y-chromosomal protein), Zp3 (zona pellucida glycoprotein 3) and Cobra1 (cofactor of BRCA1) genes. While the expression of Zfy-gene, which is required for spermatogenesis, is restricted to the testes, the expression of the Zp3-gene, which is a structural component of the zona pellucida that surrounds oocytes, is limited to the ovaries. The gene Cobra1, on the other hand, is expressed in a wide variety of tissues including ovaries and testes. As illustrated in this paper, the project culminates in presenting our results in a publicationmanuscript format, thus demonstrating our ability to assemble data into a coherent story, analyze and discuss the outcome of the experiments and set plans for future research. We believe this practice prepares us to contribute to prospective scientific investigations.