This study investigates the completeness of the reporting of infectious diseases in the prefecture of Achaia, western Greece in the period of 1999-2004. We collected hospital records relating to infectious diseases retrospectively from three major hospitals in the region and compared the records to corresponding records at the prefectural public health department (PHD). After record-linkage and cross-validation a total of 1,143 notifiable cases were identified in the three hospitals, of which 707 were reported to the PHD of Achaia, resulting in an observed underreporting of infectious diseases of 38% during the study period. At prefecture level, a further 259 cases were notified by other sources, mainly by the fourth hospital of the region not included in our study, resulting in a total of 966 cases reported to the PHD; 73% of these were reported from the three hospitals included in our study, 27% were notified by the fourth hospital not included in our study and less then 0.3% by physicians working in a private practice or health centre. Meningitis (51%), tuberculosis (12%) and salmonellosis (8%) were the most frequently reported diseases followed by hospitalised cases of varicella (7%), brucellosis (6%) and hepatitis (6%). During the study period, clustering of specific diseases like brucellosis, meningitis, mumps, and salmonellosis was observed, indicating possible outbreaks. Our results show that notification system needs to be improved, in order to ensure proper health resources allocation and implementation of focused prevention and control strategies.