Linear scleroderma en coup the sabre (LSCS), progressive facial hemiatrophy (PFH) and autoimmune encephalitis are distinct clinical entities, although patients with overlapping features have been reported. We performed a multicenter retrospective review of a series of children with LSCS and/or PFH to explore the relation between these entities. The files of 16 children were reviewed, 11 presented with LSCS, 5 with PFH, with time overlapping cutaneous features were seen. Extracutaneous signs were found in both groups. ANA were present in more than 50 % of patients. Almost half of our patients presented with CNS manifestations comprising unilateral headache, migraine and epilepsy with or without abnormalities on MRI. Brain biopsy in one patient was consistent with Rasmussen encephalitis. In two other children, associated autoimmune manifestations were present.Conclusion: Our patient cohort brings more arguments to consider LSCS and PFH as a single disease entity with LSCS and superficial skin involvement at one end of the spectrum and PFH with involvement of subcutaneous deep tissue at the other end. In both entities, encephalitis can be observed. Our findings of circulating ANA, intradermal lymphocytes and IgG, intrathecal IgG production and clinical improvement with immunosuppressive therapy endorse the concept of a possible common immune-inflammatory pathogenesis.