This study examined the effects of foundation universities on the higher education system of Turkey through perceptions of academic staff in state and foundation universities. In this qualitative research, 15 members of academic staff were interviewed for their perceptions regarding a variety of issues about foundation universities. Analysis of academic staff perceptions could be summarized as follows: staff tend to agree that foundation universities create employment opportunities; keep the students, who may otherwise have chosen to study abroad, in the country; and that they ease the financial burden of the state by providing higher education for students who may have been neglected by state universities. Increasing the number of graduates, raising quality through competition, and reversing the brain drain are also regarded as additional positive effects of foundation universities. In spite of the positive effects, academic staff also mentioned some negative aspects which could be summarized as; offering only popular programs with high job prospects in order to attract students, accepting academically challenged but affluent students which could result in a differentiation in qualifications between state and foundation university graduates. Low job security and high turnover in some departments are also of some concern. Foundation universities are not deemed to be contributing sufficiently to academic research. In addition, the interventions of founders and board members are considered to hamper the process of institutionalization and autonomy. Perceptions regarding the future of these institutions predict an increase in the number and a widening gap in quality.