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Introduction: Soon after birth, the clinical differential diagnosis between sebaceous of Jadassohn (NSJ), congenital triangular alopecia (CTA) and aplasia cutis congenita (ACC) may be challenging. A certain overlap of standard dermoscopic features can occur, especially in atypical cases, depending on scalp skin morphology and maturation age. The recently developed line-field confocal optical coherence tomography (LC-OCT) can provide morphological skin details with cellular resolution trough a rapid non-invasive examination. Objectives: To assess the LC-OCT features of 6 cases of congenital alopecia of different aetiologies, with both typical and atypical clinical appearance. Methods: A non-invasive imaging examination combining standard dermoscopy, high-resolution videodermoscopy (HRVD) and LC-OCT was realized in 7 babies presenting for congenital alopecia with overlapping features, aged between 5 months and 5 years. Results: Based on the specific LC-OCT features, and supported by HRVD features, a diagnosis of nevus sebaceous of Jadassohn (NSJ), congenital triangular alopecia (CTA) and aplasia cutis congenita (ACC) were made in 4, 2 and 1 case, respectively. Conclusions: The combined LC-OCT plus HRVD non-invasive imaging bring the advantage to have a real time diagnosis, to set the proper management and allows to avoid a skin biopsy in the perinatal age/first years of life at delicate skin site.