Clinicians caring for children with Crohn’s disease must consider the long-term implications of therapeutic interventions and cumulative diagnostic studies in their patients whose disease duration will be measured in decades. There is evidence of the increased severity of pediatric Crohn’s disease compared to its adult counterpart, its frequent co-morbid growth disturbances, and the frequent need for aggressive medical therapies including immunomodulators and biological agents. The initial management of most children diagnosed with Crohn’s disease involves enteral nutritional support, corticosteroids, and immunomodulators. Corticosteroids, while initially helpful in decreasing signs and symptoms of disease, are occasionally ineffective, generally do not heal mucosa, impair growth, and are frequently associated with a state of corticosteroid dependency. Immunomodulators are effective maintenance therapies with corticosteroid sparing effects, but have no value in the acutely ill child. The emergence of biological therapy with its impressive record of rapid efficacy and use as maintenance therapy has prompted discussion of its incorporation into initial management, but has also raised concerns about who are the most suitable candidates, which if any medications can be used concomitantly, and long-term safety. The combined use of thiopurines and anti-TNF agents may predispose to a rare and uniformly fatal lymphoma. Identification of children at high risk for complicated disease may allow us to better evaluate risk/benefit in newly diagnosed children, and biologic agents are likely to assume an increasing role in primary therapy in those deemed at highest risk. Long-term observations will determine whether biologics will change natural history and demonstrate adequate safety.