Langerhans Cell Histiocytosis (LCH) is a disease characterized by infiltration of Langerhans-type histiocytes of one or more organ systems, most commonly bone, skin, lymph nodes, liver, or lung. While localized disease tends to follow a more indolent course, multiorgan involvement is usually common in infants and portends a worse prognosis, with dysfunction of the involved organs and a mortality rate nearing twenty percent. Bone marrow involvement often presents clinically with cytopenias, however in such cases the presence of bone marrow infiltration by Langerhans cells is infrequent. We are presenting a case of a 10-month-old male child with significant pancytopenias, marked hepatosplenomegaly and scalp lesions on initial presentation. Bone marrow biopsies showed aggregates of histiocytes and evidence of hematophagocytosis without clinically meeting the diagnostic criteria for Hemophagocytic Lymphohistiocytosis (HLH). The child further developed, during his second cycle of chemotherapy, secondary HLH. Ultimately, a definitive diagnosis of multisystem Langerhans cell histiocytosis was only made following biopsy of an occipital mass, which initially was clinically considered to be a hemangioma. This case report highlights the bone marrow findings and the challenges in diagnosing multisystem Langerhans cell histiocytosis with high-risk organ involvement. It also illustrates the relationship between multisystem LCH and macrophage activation/ secondary HLH.