Osteopetrosis (OP) is a clinically and genetically heterogeneous disorder characterized by increased bone density. Associations between OP and other clinical entities are rare but include muscular degeneration, Dandy-Walker syndrome, craniosynostosis, and poikiloderma. Infantile OP has also been diagnosed in a group of infants with neuronal storage disease. An association between OP and juvenile xanthogranuloma (JXG) has never been previously reported. Herein we present a case of an intermediate form of OP in a newborn who presented with hepatosplenomegaly and pancytopenia. Histologic evaluation of a bone marrow biopsy demonstrated abnormally thickened bony trabeculae. A liver biopsy demonstrated prominent expansion of portal areas by a histiocytic infiltrate expressing CD45, CD14, CD68, CD163, factor XIIIa, and fascin, while the biopsy was negative for S100 and CD1a. These findings were those associated with JXG. Genetic testing demonstrated a mutation involving the Pleckstrin homology domain-containing family M member 1 ( PLEKHM1 ) gene. A different mutation in this gene has been previously reported in one other patient with OP. Our case is the 2nd reported case with PLEKHM1 mutation in a patient with a mild form of OP. It also demonstrates the 1st reported occurrence of OP concomitantly with JXG.