This study aimed at assessing the prevalence of soft tissue oral manifestations in children during early childhood, according to age group, gender, and site in the oral cavity, and at correlating these oral manifestations with systemic alterations. A cross-sectional study was conducted involving 586 children from 0 to 3 years of age (12.4 ± 11.8 months), 316 (53.9%) male and 270 (46.1%) female, in the city of Mauá, SP, Brazil. Examination was performed by a single examiner (Kappa Index = 0.90) according to World Health Organization criteria (WHO, 1997).The prevalence of oral manifestations in the soft tissues of children during early childhood was 34.8%. The age group showing statistical significance was 0-1 months old (56.4%). Epstein’s pearls were significantly present (43.2%) in 0-1-month-old babies, and gingivitis in 12-24-month-olds (15.9%). The palate was the most affected region (16.7%). Infectious alterations were the most prevalent systemic alteration (20%). An association was observed between the presence of systemic alterations and the occurrence of oral manifestations. The prevalence of oral manifestations was 34.8%, regardless of gender, and was manifested mostly in 0-1-month-old babies. The palate was the most prevalent region, and the majority of oral manifestations were associated with systemic alterations.