High faculty morale and job satisfaction are vital for optimum performance and important to the quality and vitality of the academic enterprise. However, research on faculty morale and job satisfaction has historically been limited to faculty at traditional comprehensive institutions and specific professional programs. Faculty who conduct biomedical research at academic health centers experience substantial differences in employment expectations and how they are funded than other faculty. The purpose of this study was to explore how personal and professional factors contribute toward positive morale and job satisfaction for faculty in biomedical research programs at one academic health center. This qualitative study used individual semi-structured interviews to explore work-life aspects associated with self-reported levels of morale and job satisfaction. Results from this study indicated that biomedical research faculty enjoy their work and highly value collaborating with their colleagues. The persistent need to fund at least half of their salaries through soft money, the loss of valued colleagues due to turnover, and a lack of identity with their institution decreases job satisfaction. It was also found that job satisfaction is expressed differently by gender and length of employment at one's current institution. Female faculty expressed feelings of limited support for those raising families while faculty employed longer expressed lower satisfaction than those recently hired. Better understanding of what influences job satisfaction and morale for this population will help academic health centers further support their research faculty as well as increase positive faculty identification with the institution.