Introduction Inflammatory bowel diseases (IBD) have classically included two entities: Crohn's disease (CD) and ulcerative colitis (UC). The correct differentiation between these two diseases has important implications. The term inflammatory bowel disease unclassified (IBDu) describes inflammatory changes of the colon that cannot be classified as ulcerative colitis or Crohn's disease. This situation has been described in 20-30% of paediatric IBD at diagnosis. In order to reach a definitive diagnosis of suspicion of inflammatory bowel disease in children, the ESPGHAN (European Society for Paediatric Gastroenterology, Hepatology and Nutrition) established the Porto criteria (PC) in July 2005. The recommendations include: 1) total colonoscopy with ileal intubation, 2) upper endoscopy, 3) multiple biopsies and 4) complete small bowel exploration. Aim To evaluate the diagnostic procedures used in our IBD patients regarding the PC. Patients and methods Retrospective review of the data of our IBD patients diagnosed in the last ten years (1999-2008) in a Spanish tertiary hospital, differentiating two periods: before and after the publication of the PC. Results A total of 108 IBD patients had been diagnosed (51 UC, 52 CD, 5 IBDu), 43 girls (39.81%), 65 boys (60.18%). According to the Montreal classification: 1) UC, 40 (78%) extensive colitis, 5 left-sided colitis (9.8%), 6 proctitis (11%), 2) CD: 44 ileo-colonic (84%), 13 ileal, 7 colonic. Median age at diagnosis: 13 years 1 month (p25-p75: 10 years 3 months- 14 years 9months). The Porto criteria were followed in 49% of the cases (33.3% before its publication, 64.8% after, P = .001). Upper endoscopy was performed in 62 patients (58%): 38.9% versus 72.2%, P < .001. Upper involvement was found in 51% of our CD patients. Total colonoscopy with ileoscopy was achieved in 85.2% of the cases. The mean number of ileo-colonic segments biopsied was 6.6 (7 different segments). Granulomas at biopsies were present in 38% of our CD patients. Up to 38% of the CD patients had microscopic inflammation in endoscopically normal appearing segments. During the follow-up, initial diagnosis among the IBDu patients, was changed to CD in 1, to UC in 2 and the other 3 remained with the same diagnosis. We did not observe other changes in diagnosis in the remaining 103 patients (median follow-up: 4y 8mo). Thirty patients were discharged when becoming adults. Conclusions Our clinical practice in IBD diagnosis has changed after the PC. Upper endoscopy is a useful tool to find upper involvement in CD. Total colonoscopy with ileoscopy and performance of multiple biopsies are essential to determine extension of the inflammatory changes. We have not observed changes in the final diagnosis in our CD and UC patients after a median follow-up of 4 years.