The incidence of Crohn’s disease (CD) has been reported to increase. The aim of this review is to perform a comprehensive literature search of population-based studies focused on the natural history of paediatric-onset CD. A literature search of English and non-English language publications listed in the electronic database of MEDLINE (source PUBMED) and EMBASE from 1935 to 2016 was performed. Population-based studies or national cohorts reporting data on the short-term or long-term disease course of paediatric CD were included. Forty-nine paediatric and 15 nonpaediatric studies on CD have been identified. Up to one-third of children with inflammatory behaviour developed bowel complications more than 5 years after diagnosis. From 48 to 88% of children have experienced at least one corticosteroid course irrespective of the period of diagnosis and up to one-third became steroid dependent. Immunosuppressive preparations were used earlier and more frequently in newer than older cohorts (68 vs. 32% at 5 years) and more than one-third of children have received biological treatment early in the disease course. A decline in the surgery rate might be observed in more recent compared with older unselected populations. The relative risk of cancer in childhood-onset CD as well as the risk of death seem to have increased. Childhood-onset CD seems to be an aggressive phenotype of the disease. Compared with older cohorts, a trend towards decreasing surgical rate can be observed in newer cohorts paralleled by an increase in immunomodulator use and biologicals. Nevertheless, the causative role has yet to be investigated.