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Objective Little is known about the transmission of coronavirus disease 2019 (COVID-19) in young children. This study aimed to clarify the risk of COVID-19 transmission among this population. Methods Between July 2020 and April 2022, 1660 0 to 3-year-old children underwent a nasopharyngeal swab for later reverse transcription-polymerase chain reaction testing at a mass screening test center in Japan. Their disease transmission rate and clinical symptoms were evaluated according to the predominant variant strains of that season. Results The secondary transmission rate after close contact of the Delta B.1.617.2 (17.4%) and Omicron B.1.1.529 (39.2%) variants was significantly higher than that of the conventional strains (B.1.1.284 and B.1.1.214; 4.5%) during the pandemic. The increased transmissibility with the Delta and Omicron variants was independent of close contact or location. The prevalence rates of cough, fatigability, and fever were similar in young children infected by the Delta and Omicron variants. Conclusions COVID-19 transmission in children aged 0 to 3 years increased by 3 to 4 fold during the Delta outbreak and by 8 to 10 fold during the Omicron outbreak compared with the conventional strain outbreak. The symptoms in young children were not different between the Delta and Omicron variants.