Abstract Background The Brazilian Organization for Crohn's Disease and Colitis (GEDIIB) has established a national registry of inflammatory bowel disease (IBD). Timely diagnosis and treatment of the disease are crucial to mitigate the risk of complications in this patient population. Therefore, this study aimed to assess the variables associated with delayed diagnosis and the frequency of complications in IBD patients in Brazil. Methods A cohort study was conducted from August 2020 to August 2023. Data were obtained from medical records and patient consultations using the REDCap platform, with approvals from the ethics boards of participating institutions. Patients were categorized based on the time from symptom onset to diagnosis: < 1 year, 1 to 1 year 11 months, and ≥ 2 years. Socioeconomic and clinical data, such as disease extension, use of biological therapy, and complications like the need for surgery or hospitalization, were evaluated. Results The study included 2,436 patients, with 1,147 diagnosed with ulcerative colitis (UC) and 1,289 with Crohn's disease (CD). Of these, 62% were managed in public centers, and 38% in the private system. The age at diagnosis was 38 ± 15.5 years for UC and 33.7 ± 14.9 years for CD, with females predominating (64.5% for UC and 53.4% for CD). Among UC patients, disease extension included pancolitis (43.5%), left colitis (28.8%), and proctitis (27.7%). The time between symptom onset and diagnosis was longer in CD patients (p<0.001), as follows: < 1 year (UC 58.4% and CD 50.9%), 1 to 1 year 11 months (UC 22.3% and CD 21.1%), and ≥ 2 years (UC 19.3% and CD 28%). The shortest interval in UC patients was observed in private services (p<0.001), Southern and Northeastern regions of Brazil (p<0.001), and in patients without extraintestinal manifestations (EIM) (p=0.003). No differences were noted regarding disease extent, need for surgery, hospitalization, presence of cancer, or use of biological therapy. In CD patients, the shortest interval was observed in private services (p<0.001), the Southern region of Brazil (p<0.001), and was associated with a lower rate of hospitalization due to complications or disease activity (p=0.032). Among those who underwent surgery (35.6%), patients operated on in a public university hospital experienced a greater delay in diagnosis (p=0.014). No differences were observed regarding the presence of perianal disease, need for surgery, cancer, or use of biological therapy. Conclusion The window of opportunity is imperative to reduce complications, especially in CD. Further epidemiological studies are needed to shape national public health policies, emphasizing early diagnosis and appropriate treatment of IBD.