BackgroundThe importance of physical activity in the first months of age is well known, however, with the evolution of the urban environment, the excessive workload of parents and the excessive time in growing up in kindergartens has limited this same free practice and little has been studied about this issue. In Portugal, there are institutions that provide oriented physical activity for their children, however, this is optional, which may create disadvantages in children’s motor skills in these ages.ObjectiveThe objective of the study isto verify if there are differences in the development of motor skills (global and fine) comparing children between 12 and 48 months who practice oriented physical activity (OPA) and children who do not.MethodsParticipated in this study, 400 children of both genders (28.14 ± 7.23 months). Two groups were created (the group that had oriented physical activity (30 min long and 2 times a week) and the group that didn’t have oriented physical activity). For a better understanding they were divided into 3 age groups (12–23, 24–35 and 36–48 months). Motor skills were assessed using the PDMS-2 scales, for 6 months, following the instrument’s application standards.ResultsIn a first analysis, we found that the majority of children only start to practice oriented physical activity in institutions from 36 months of age, however, it is in the first months (from 12 to 35) that the greatest differences between the two groups can occur. The OPA group presented better results according to the mean values, in all motor skills. Differences between groups were most noticeable in Postural, locomotion and fine manipulation Skills (showing effect size: moderate and low).ConclusionsWe can conclude that a practice of oriented physical activity in the first 48 months is fundamental to the development of motor skills. It is in the first months (up to 36) that there are greater differences, but it is also where there are less children carrying out guided physical activity. This is an important factor, and is determinant to make institutions aware of this importance of this variable in child development.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12887-023-04060-8.