The organizational appropriateness of hospital stays is an expression of a hospital's efficiency and aim of the management control. The AEP (American Version)/PRUO (Italian Version) protocol is specific for measuring the organizational appropriateness of hospital stays. The aim of this study is the comparative analysis of the organizational appropriateness of hospital stays in Careggi Hospital of Florence and in all hospital Departments in 1995 and 1998. In 1998 the AEP/PRUO protocol was applied to 2148 samples of hospital stays out of 38,968 eligible hospitalizations, and in 1995 a sample of 1989 hospital stays out of 35,108. In 1998 2,148 admissions and 15,338 days of hospitalization were tested. In 1995, 1989 admission days and 12,264 days of hospitalization were tested, 63 departments were studied. In 1995 the first edition of the protocol was applied, in 1998 the second. A sample of 218 of the 1998 hospital stays was tested with both editions to evaluate the impact of differences. In 1998, with the second edition of the protocol, the inappropriateness rate of admission days and hospitalization days and the rate of in-patients inappropriate hospital stays was respectively 38.0%, 43.8% and 18.5%. Compared with 1995 results, the rates increased +6.2%, 6% and +7.5% respectively. Instead, with the first edition of the protocol, the rates were 29.7%, 37.6% and 10.7% and, compared with 1995, they were reduced -2.1%, -0.6% and -0.3%. The longitudinal multilevel analysis has allowed the evaluation of the performance of each department.