Background: The primary aim of the study was to estimate the incidence of Crohn's disease (CD) and ulcerative colitis (UC), collectively known as inflammatory bowel disease (IBD), in Malta in a well-defined population during a 13-year study period.Methods: Diagnostic criteria for CD and UC were defined. A diagnosis of IBD was obtained from the histopathology reports at St. Luke's Hospital, Malta, between January 1993 and December 2005. The date of diagnosis was defined as the date of the first histopathology report revealing signs of IBD.Results: Incidence rates were standardized using the direct method on the European Standard Population. The mean incidence of UC in males was 8.16 per 100,000 per year and for females was 7.59 per 100,000 per year, while that for CD in males was 0.96 per 100,000 per year and for females 1.622 per 100,000 per year. Using linear regression, in UC there is an almost significant (P = 0.069) increasing trend with time but no difference by gender (P = 0.591). On the other hand, in CD there is no significant trend with time (P = 0.555) but almost a significant difference by gender (P = 0.078).Conclusions: This is the first Maltese study in which the incidence of IBD has been recorded. In Malta the incidence of UC is similar to the overall incidence of other European countries while the incidence of CD is lower. In fact, the incidence rates of CD are among the lowest in Europe, similar to other southern European countries.