Background To identify the patterns of lifestyle behaviours in children aged 3 years, to investigate the parental and child characteristics associated with the lifestyle patterns, and to examine whether the identified lifestyle patterns are associated with child BMI and weight status. Methods Cross-sectional data of 2090 children 3 years old participating in the Dutch BeeBOFT study were used. Child dietary intakes, screen times and physical activity were assessed by parental questionnaire, and child weight and height were measured by trained professionals according to a standardized protocol. Latent class analysis was applied to identify patterns of lifestyle behaviours among children. Results Three subgroups of children with distinct patterns of lifestyle behaviours were identified: the ‘unhealthy lifestyle’ pattern (36%), the ‘low snacking and low screen time’ pattern (48%) and the ‘active, high fruit and vegetable, high snacking and high screen time’ pattern (16%). Children with low maternal educational level, those raised with permissive parenting style (compared those with authoritative parents), and boys were more likely be allocated to the ‘unhealthy lifestyle’ pattern and the ‘active, high fruit and vegetable, high snacking and high screen time’ pattern (P < 0.05). No association was found between the identified lifestyle patterns and child BMI z-score at age 3 years. Conclusions Three different lifestyle patterns were observed among children aged 3 years. Low maternal educational level, permissive parenting style and male gender of the child were associated with having unhealthy lifestyle patterns for the child.