BACKGROUND: We aimed to explore the epidemiology of inflammatory bowel diseases [IBD] in association with the COVID-19 pandemic in two countries with different lockdown policies. METHODS: We utilized nationwide IBD cohorts in Israel and Sweden to explore the incidence of IBD during the pandemic compared to 3 years prior [2017-2019]. We examined temporal trends through the presence of inflection points by Joinpoint regression analysis and reported average monthly percentage changes [AMPC]. RESULTS: A total of 155 837 patients with IBD were included [Israel, 58 640; Sweden, 97 197]. The annual incidence of IBD was stable until 2019 in both countries but then decreased in Israel (AAPC -16.6% [95% confidence interval, CI, -19.9% to -10.0%]) and remained stable in Sweden (AAPC -3.5% [95% CI -11.6% to 3.7%]). When exploring the monthly incidence during the pandemic, in Israel the rate remained stable until November 2020 (AMPC 2.3% [95% CI -13.4% to 29.9%]) and then decreased sharply (AMPC -6.4% [95% CI -20.8% to 17.0%] until February 2021 and to -20.1% [95% CI -38.9% to -4.7%] from February 2021), while in Sweden, which had a less stringent lockdown policy, it decreased slightly until July 2020 (AMPC -3.3% [95% CI -21.6% to 20.3%]), but increased thereafter (AMPC 13.6% [95% CI -12.6% to 27.0%]). The change of incidence rate in Sweden occurred mainly in elderly-onset patients, the only population with significant restrictions during the pandemic. CONCLUSION: The incidence of IBD decreased during the pandemic in association with lockdowns, more so in Israel, which had more stringent policies. Future studies are needed to determine the long-term effect of the pandemic on IBD.