ABCA3 deficiency is a rare cause of neonatal respiratory failure. Biallelic complete loss of function variants, mainly nonsense or frameshift mutations, result in a total absence of ABCA3 function and lead to a fatal outcome without lung transplantation. However, children with ABCA3 variants with a partial biological activity have variable outcomes. For these variants, the discrimination between pathogenic or benign effects is crucial to better define the clinical outcomes and to define the most appropriate treatment approach and to lead the genetic counseling. In our study, the clinical course of 3 children carrying biallelic ABCA3 mutations and presenting respiratory distress at birth has been described. In-silico analysis of ABCA3 protein structural alteration due to different variants has been performed by the tools SIFT (sorting intolerant from tolerant) or PolyPhen2 (polymorphism phenotyping version 2) that predict the impact of amino acid substitution on protein conformation. The analysis showed that the type and localization of the variants in the domains of ABCA3 protein could predict the clinical outcome. The records (clinical presentations, diagnostic imaging, and prescribed treatments) of three children with ABCA3 mutations evaluated at Bambino Gesù Children Hospital between January 2017 and January 2023 were re-examined to correlate the clinical information with the effects of the variants on ABCA3 structures and functions. Our data indicate that information on ABCA3 protein 3D structure could help in predicting the impact of mutations on ABCA3 biological activity and, therefore improving the diagnosis by facilitating the choice of a specific therapy.