Background: organisational culture is the character of the environment of individual bodies. It consists of a set of values, norms and customs that govern the relations between people within it. Its elements are a mission or goals, organisational climate and a working atmosphere, which affect motivation, effectiveness and, ultimately, management style. Aim: this research aimed to determine which organisational culture is prevalent in hospitals, and which staff consider is the most desirable. Methods: the research was conducted in two hospitals in Zagreb—University Hospital Sveti Duh and University Hospital Dubrava. The Organizational Culture Assessment Instrument was administered to 87 nurses. Results: in both hospitals, a clan culture was prevalent, followed by a hierarchical culture, then a competitive culture. The adhocracy culture was the least common. Participants said a clan culture was the most desirable, then a hierarchical culture, followed by the adhocracy culture; the least desirable was a competitive culture. In Sveti Duh, a clan culture was predominant, while in Dubrava it was a hierarchical culture. The most desirable culture for staff of both hospitals is the clan culture, but it was more prevalent in Sveti Duh. Conclusion: in two Croatian university hospitals, according to staff, a clan organisational culture is the most common type and is also the most desirable.