Researchers hypothesize that the disruption in the bacteria in the gut caused by antibiotics might be to blame for this increase in cases of IBD. The gut flora is not well established until after the first year of life, so use of antibiotics in infancy has a more profound effect on the gastrointestinal tract than antibiotic use later in life.
This is a very small study, and larger studies would need to be done in order to confirm the results. The authors also state that results could be confounded because children who need antibiotics so early in life might already be predisposed to developing IBD.
Source:
Shaw SY. "Antibiotic Prescriptions in the First Year of Life Increases the Risk of Pediatric Inflammatory Bowel Disease: A Population-Based Analysis (Abstract #95)." Digestive Disease Week 2010. 18 May 2010.

