Rapid notification of infectious diseases is essential for prompt public health action and for monitoring of these diseases in the Irish population at both a local and national level. Anecdotal evidence suggests, however, that the occurrence of notifiable infectious diseases is seriously underestimated. This study aims to assess the level of hospitalization for notifiable infectious diseases for a 6-year period in one health board region in Ireland and to assess whether or not there was any under-reporting during this period. All hospital in-patient admissions from 1997 to 2002 inclusive with a principal diagnosis relating to 'infectious and parasitic diseases' (ICD codes 001-139) of residents from a health board region in Ireland were extracted from the Hospital In-Patient Enquiry System (HIPE). All notifiable infectious diseases were identified based on the 1981 Irish Infectious Disease Regulations and the data were analysed in the statistical package, JMP. These data were compared with the corresponding notification data. Analysis of the hospital in-patient admission data revealed a substantial burden associated with notifiable infectious diseases in this health board region: there were 2758 hospitalizations by 2454 residents, 17,034 bed days and 33 deaths. The statutory notification data comprises both general practitioner and hospital clinician reports of infectious disease. Therefore, only in cases where there are more hospitalizations than notifications can under-reporting be demonstrated. This occurred in nine out of 22 notifiable diseases and amounted to an additional 18% of notifications (or 572 cases) which were 'missed' due to hospital clinician under-reporting. The majority of these under-reported cases were for viral meningitis (45%), infectious mononucleosis (27%), viral hepatitis C unspecified (15%) and acute encephalitis (5.8%). This study has highlighted the extent of under-reporting of hospitalized notifiable infectious diseases, in a health board region in Ireland, which is a cause for concern from a surveillance point of view. If this under-reporting is similar in other health boards, then it would appear that the epidemiology of some notifiable diseases is incomplete both regionally and nationally. This under-reporting negatively impacts on the effectiveness of the notification process as a 'real-time' surveillance tool and an early warning system for outbreaks.