Background and objectives: The COVID-19 pandemic has drawn attention to the Coronavirus family of viruses. However, in community settings there is relatively limited information on these viruses in healthy children. Our objective was to explore the epidemiology of the four endemic (non-SARS-CoV-2) human coronaviruses (HCoV) by species, including acute illness episodes, risk factors and healthcare burden in a cohort of Australian children in the first 2-years of life. Methods: The Observational Research in Childhood Infectious Diseases (ORChID) community-based cohort was a prospective study describing acute respiratory illnesses in children from birth until their second birthday. Parents recorded daily symptoms, maintained an illness-burden diary and collected weekly nasal swabs, which were tested for 17 respiratory viruses, including HCoVs, by real-time polymerase chain reaction assays. Results: 158 children participating in ORChID provided 11,126 weekly swabs, of which 168 were HCoV positive involving 130 incident episodes. HCoV-NL63 and HCoV-OC43 were most commonly detected and accounted for two-thirds of episodes. While 30 children had different HCoVs detected on different occasions, seven were reinfected with the same species 4–16 months later. The incidence of HCoV in the first 2-years of life was 0.76 episodes per child-year (95% confidence interval [CI] 0.63–0.91) with incidence greatest in the second year (1.06; 95%CI 0.84–1.33) and during Winter (1.32; 95%CI 1.02–1.71). Only 50% of HCoV episodes were symptomatic, of which 48.4% led to healthcare contact. Conclusions: In children, HCoV infections are common, recurrent and frequently asymptomatic. Future studies should determine transmission pathways and immune mechanisms.