Physical sciences and engineering doctoral programs serve as the most important conduit through which future academics are trained and prepared in these disciplines. This study examined women doctoral students' protege-mentor relationships in Physical sciences and engineering programs. Particularly, the study examined the influence of such relationships on this group of women's academic career aspirations. A qualitative approach and ethnographic traditions were utilized to explore women doctoral students' mentoring activities in physical sciences and engineering programs. In-depth ethnographic interviews were conducted between 25 women doctoral students and 10 faculty members from both genders from a large research university in the western region of the U.S. Data was analyzed based on both a deductive approach guided by theory and an inductive technique that reflects the themes, which emerged from the data. The major findings of this dissertation study relate to women's experiences, challenges, and coping strategies; and shed light on the current state of protege-mentoring relationships in physical sciences and engineering departments at one research university in the western U.S. The findings highlight the nature of the protege-mentor interactions and the influence such relationships have on women's decisions concerning the pursuit of academic careers. Further, though unexpected at the design stage of this study, the importance of community emerged as one of the major findings. The formation of communities of support seems a rather important strategy for women doctoral students in the process of graduate school socialization; this source of support appears critical to further developing protege-mentor relationships, increasing one's ability to publish, engage in research collaborations, and advance one's career interests. It appeared to be the most important strategy that women doctoral students utilize when they experience dysfunctional advising relationships. Many women's career related concerns and their pursuit of helpful advice were provided by a meshwork of women scientists and engineers whom they met at conferences, cross-institutional research collaborations, and through a range of diverse channels and networks. In many cases, these included those developed during their undergraduate studies. Informal socialization was very impactful when it came to women's career decision-making process. Yet, this is the aspect of protege-mentor relationships that has been mostly overlooked by faculty in physical sciences and engineering departments at Western Research University (WRU). Women faculty interviewed for my study were more likely to be involved in the informal socialization process to mentor women doctoral students and address work-life balance concerns. Some male faculty expressed negative attitudes toward women doctoral students' non-academic career trajectories and tended to ignore work-life balance concerns. They demonstrated these attitudes in daily interactions and research meetings with their students. This created an environment in which it was difficult for women to discuss their doubts about pursing academic careers with their faculty advisors. This study revealed some hidden barriers that many women doctoral students face in the process of pursuing a doctorate and an academic career. These barriers took the form of implicit gender bias, complex and confusing environments for negotiating unequal treatment, dysfunctional advising, particularly in the areas of career development and work-life concerns, and subtle and covert forms of sexual harassment. Acknowledging these unique challenges that women doctoral students in physical sciences and engineering programs face is the first step to assist them, but more direct efforts also most be employed to create an environment more conducive to the success of women in science. Department faculty and academic leaders have a unique and important role to play in addressing such matters. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]