The purpose of this study was to estimate the incidence and prevalence of Crohn's disease (CD) in South-Muntenia, Bucharest-Ilfov and the Southwest region, using data collected from the main referral center in the area, during 2005-2009.Materials and methods A retrospective, descriptive study was conducted based on the 593 patients with CD admitted to the Center of Gastroenterology and Hepatology, Fundeni Institute, during this period. The incidence and the prevalence were reported per 100,000 inhabitants aged over 18.Results The incidence and the prevalence between 2005-2009 were estimated at 0.49 /100,000 and 1.88 / 100,000 inhabitants respectively. They both described an oscillating trend between 2005-2009, increasing in 2009 by 32% (p = 0.036) and by 69% (p = 0.000) respectively, as compared to 2005. The sex specific incidence rates was slightly, but not significantly, higher among women (0.59) than men (0.49). The average age at admission was 44. A bimodal age distribution was noticed with two peaks: between 30-39 and 50-59 years old. The highest incidence rate was found in the urban areas (1.09) and Bucharest (0.7). The temporal trend analysis showed that incidence of CD does not suffer significant changes over the interval 2010-2014, predicting an annual incidence rate of 0.52 / 100,000.Conclusion Data collected in the main referral center for the South-Muntenia, Bucharest-Ilfov and Southwest regions during the last five years confirms the previously described low frequency of CD in Romania, the bimodal age distribution and later onset of disease. The male to female ratio is close to unity, suggesting that men and women are generally at similar risk. There is a significant increase in both incidence and prevalence of CD when comparing 2005 with 2009. In term of predicting trends, the incidence of CD appears to be relatively stable, whereas the prevalence understandably rises over the interval 2010-2014. A further prospective multicenter study is necessary in order to assess the precise incidence, prevalence CD in Romania and to make more accurate predictions regarding future trends.