Background: The aim of this study was to describe the incidence of inflammatory bowel disease (IBD) and changes in demographic and phenotypic disease presentation in Otago, New Zealand. Methods: This study was conducted at Dunedin Hospital and the study period was 1996–2013. Otago residents diagnosed with IBD were identified retrospectively from hospital lists using ICD-10 codes. Diagnosis, and place and date of diagnosis, were confirmed using medical notes and histology reports. Demographic, clinical and diagnostic data were recorded. Age-standardised incidence rates were estimated and trends over time assessed. Multinomial logistic regression was used to assess evidence for any changes in the distribution of disease location for Crohn’s disease (CD) cases. Results: The diagnosis of IBD was confirmed in 224 males and 218 females, and most were New Zealand European. Of the total number of confirmed IBD cases, 40.0% were ulcerative colitis (UC), 52.1% were CD and 7.9% were IBD unclassified. The age distribution illustrated bimodal peaks at 20–24 years and 65–69 years. Incidence rates varied from year to year, but there was no statistically significant change over the 18-year study period. The estimated age-standardised IBD incidence varied between 5.8/100,000 in 2006 and 29.8/100,000 in 2012. The incidence rates for UC and CD were 2.8/100,000 and 1.8/100,000, respectively, in 2006 and 6.3/100,000 and 21.8/100,000, respectively, in 2012. There were no significant phenotypic changes in CD patients over the study period. Conclusions: The IBD incidence in Otago, New Zealand, is high compared to many other countries. Annual age-standardised incidence rates vary, highlighting the limitations of single-year incidence data.