Inflammatory Bowel disease (IBD) is traditionally divided into Crohn’s disease (CD) andulcerative colitis (UC). UC is a relapsing non-transmural inflammatory disease that isrestricted to the colon and is characterized by flare-ups of bloody diarrhea. CD is achronic, segmental localized granulomatous disease that can affect any part of the entiregastrointestinal tract. Ileo-anal pouch is a procedure restoring functionality of the rectumafter a colectomy. IBD is a multifactorial disease and flaresof IBD are probably triggeredby changes in the intestinal microbiota followed by an abnormal immune response. In thisstudy, we aim to analyze the intestinal bacterial diversityin IBD patients during variousstages of disease compared with healthy controls. Permission for human experimentsand recruitment of participants was obtained from the EthicCommittee for CopenhagenCounty hospitals (Permission no. KA-03019, Permission no.KA-20060159). Stoolsfrom 26 healthy controls, 42CD, 38 UC and 18 pouch patients were collected. StoolDNA extraction was performed using Qiagen, DNA mini stool kit Denmark. DGGE-PCRamplifying the V2-V3 region of 16S-rDNA gene of the bacteriawas amplified by universalprimers HDA1 and HDA2. Analysis of DGGE was performed blinded using BioNumericsversion 7.5. After normalization, a DGGE gel band matching was performed. Thesimilarities between profiles were calculated with a rankedPearson correlation coefficientbased on the band matching results using band intensities. Simpson’s index of diversityand Pielou’s species evenness were calculated. Based on theShannon Diversity Index,UC patients had lower species diversity and bacterial evenness in comparison to healthypersons,p<0.05. However, only CD and disease pouch patients had lower speciesdiversity compared to those with inactive disease and healthy controls. Well-functioningpouch patients had decreased species evenness in comparison to diseased pouchpatients and control group. During the active disease stagein CD and pouch, the patientshave a low bacterial diversity in their gut when compared to the inactive stage. In UCpatients, a generally low diversity was observed at all stages of the disease compared tohealthy controls.