The purpose of this study was to explore key attributes of service quality in the Croatian higher education system. In particular, the study aims to compare student and faculty perceptions of service quality and to identify institutional aspects that may affect the perceptions of these two customers. Principal component analysis is used to define key dimensions of service quality and independent sample t test or one-way between groups ANOVA to analyse the impact of institutional aspects on customer perceptions. The findings of this study showed that students and faculty separate service quality dimensions in a similar manner. The study also provides insight into the effects of institutional aspects on customer perceptions. The results revealed that ownership status, research orientation, and size significantly moderate customer perceptions of the service quality. The findings reported in this paper draw attention to the importance of the customer perceptions in the higher education context and the role of institutional characteristics in the formation of customer perceptions.