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Despite remarkable progress in diagnosis and understanding the pathogenesis of rare diseases, their management still remains very difficult and reserved especially for specialized medical center. Skin disorders [(systemic phacomatosis pigmentovascularis (PPV) and persistent lymphadenopathy (Kikuchi-Fujimoto disease (KFD)] are two rare conditions in the pediatric age. We describe an 11-year-old boy with congenital phacomatosis pigmentovascularis suffering from fever, nocturnal perspiration, fatigue, poor appetite and right cervical lymphadenopathy. The predominance of systemic symptoms prompted an extensive investigation. The diagnosis of PPV was confirmed by physical examination and MRI, and diagnosis of KFD was made after direct histological examination of a lymph node biopsy. Seeing the low prevalence of these two diseases, it becomes important that a prompt and correct diagnosis is required to minimize unnecessary investigation and the inappropriate instigation of potentially harmful treatments as well as providing reassurance to the child, parents and doctors involved.