Enhancing the diversity of the scientific workforce is critical to achieving the mission of NIH: "To seek fundamental knowledge about the nature and behavior of living systems and the application of that knowledge to enhance health, lengthen life, and reduce the burdens of illness and disability." However, specific groups have historically been, and continue to be, underrepresented in the biomedical research workforce, especially academia. Career choice is a multi-factorial process that evolves over time; among all trainees, expressed interest in faculty research careers decreases over time in graduate school, but that trend is amplified in women and members of historically underrepresented racial and ethnic groups (Fuhrmann, Halme, O'Sullivan, & Lindstaedt, 2011; Gibbs, McGready, Bennett, & Griffin, 2014; C. Golde & Dore, 2004; Roach & Sauermann, 2017; Sauermann & Roach, 2012). Neuroscience as a discipline has characteristics that may exacerbate the overall trends seen in the life sciences, such as a greater growth in the number of awarded neuroscience PhDs than in other life sciences fields (US National Science Foundation, 2016b). This work was designed to investigate how career interest changes over time among recent neuroscience PhD graduates, and whether differences in career interests are associated with social identity (i.e. gender and race/ethnicity), experiences in graduate school and postdoctoral training (e.g. relationship with advisor; feelings of belonging), and personal characteristics (e.g. confidence in one's potential to be an independent researcher). We report results from a survey of 1,479 PhD neuroscientists (including 16% underrepresented (UR) and 54% female scientists). We saw repeated evidence that individual preferences about careers in general, and academic careers specifically, predict current career interest. These statistically significant preferences mostly had medium to low effect size that varied by career type. These findings were mediated by social identity and experiences in graduate school and postdoctoral training. Our findings highlight the important influence of the advisor in shaping a trainee's career path, and the ways in which academic culture is perceived as unwelcoming or incongruent with the values or priorities of certain groups. For women, issues of work/life balance and structural issues of academia, and for UR women in particular, lower confidence in their ability to be an independent researcher, affected their interest in academia. Both women and UR men in our study report a lower importance of autonomy in their careers. UR respondents report feeling less like they were a part of the social and intellectual community. However, they have formed beneficial relationships with faculty outside their PhD institutions that, particularly for UR women, are associated with increased interest in academia. Our findings suggest several areas for positive growth, ways to change how we think about the impact of mentorship, and policy and programmatic interventions that extend beyond trying to change or "fix" the individual and instead recognize the systemic structures that influence career choices.