The analysis of functional abilities and their development in early childhood (0-6 years old) are fundamental aspects among young children with certain types of developmental difficulties that can facilitate prevention, through programmed interventions adapted to the needs of each user (student or patient). There are, however, few investigations to date, that have analyzed the use of automated tools for recording and interpreting the results of the initial assessment. Here, a protocol is presented to examine the functional abilities in early childhood in young children, aged between 3-6 years old, with intellectual disabilities, but the protocol can also be used for ages 0 to 6 years. The protocol makes use of a computer application, eEarlyCare, that facilitates the interpretation of the results of systematic observations, which are recorded in natural environments by professionals trained in early intervention. The software can be used to analyze 11 functional areas (Food Autonomy, Personal Care and Hygiene, Dressing and Undressing Independently, Sphincter Control, Functional Mobility, Communication and Language, Daily Life Routines, Adaptive Behavior and Attention) and a total of 114 different behaviors. Its use facilitates the analysis of the observed abilities and greatly assists early intervention. Compared to other observational methods, it allows a more efficient use of personal and material resources. The use of the computer application facilitates the recording of the observation results, which helps with organization and reflection on the observations. The software displays the observation results on-screen compared to normal developmental parameters. This information can be referred to for decision-making about the most suitable intervention program for each user (student or patient). Likewise, clustering techniques are applied to analyze the relation between the type of intellectual disabilities and functional development identified with the software, a relation that is intended to serve as a guide for early-care professional intervention.