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It often begins as small inflammatory lesions in the first 2 layers in the gut, but eventually spreads, reaching all layers (although the submucosa, or second layer, is hit the hardest). Cracks (fissures) and crevices develop in the tissue, and swelling occurs. This combination gives a cobblestone appearance (seen below).
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A major concern that arises later in disease progression is poor nutrition. The tissue in the gut is special - it absorbs all the nutrients we require from food as it passes through. In Crohn's, the swelling and hardening of tissue disrupts the tissue's flexibility and ability to absorb nutrients as effectively, resulting in poor nutrition. This can be detrimental in children, especially early on, as much growth and development occurs early in life (and can be stunted by early progression of the disease).
33% of Crohn's patients also develop either a perirectal abscess, fissure, or fistula. A fistula is a tunneled connection between two organs, such as a tunnel connecting the intestine of the gut to the vagina, called an enterovaginal fistula (pictured below).
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Unfortunately, within the first 10 years of the disease, about half of Crohn's patients will develop a fistula, while 80% will require some type of surgery over their lifetime.
References:
Smith, C., & Harris, H. (2014, December 1). Crohn disease: Taking charge of a lifelong disorder. Nursing 2014, 37-38.