Nasopharyngeal carcinoma (NPC) is a polygenic inheritance disorder. Both environmental and genetic risk factors play important roles in NPC carcinogenesis and progression, and there are complex interactions between genes and environmental carcinogens. Whole-genome loss of heterozygosity analyses and comparative genomic hybridization analyses identified that the short arm of chromosome 3 were high-frequency deleted in NPC biopsies, and genetic linkage analyses of human NPC families identified chromosome 3p21 as a new susceptibility gene region. Using phenotype cloning strategy, we identified LTF as a tumor suppressor and susceptibility gene of NPC on chromosome 3p21. Lactotransferrin, encoded by LTF gene, is an innate immune protein that widespreadly secreted into most biological fluids including mammal milk, nasal secretions, tears, etc. LTF was highly expressed in normal nasopharynx and significantly down-regulated in NPC tissues and down-regulation of LTF was correlated with progression, invasion and metastasis of NPC. A case-control study implied that two single nucleotide polymorphisms (SNPs) in LTF gene affect the expression level of LTF, and associated with NPC risk. We found that lactotransferrin could protect human primary B lymphocytes and nasopharyngeal epithelial cells from Epstein-Barr virus (EBV) infection by binding to CD21, the EBV receptor on B lymphocyte surface, blocking the infection of EBV into B cells and inhibiting the transfer of EBV from B cells to nasopharyngeal epithelial cells. In addition, lactotransferrin could reduce the EBV stimulated inflammatory responses and protect nasopharyngeal epithelial cells from carcinogenesis. We also found that lactotransferrin could inhibiting the proliferation and metastasis through MAPK and AKT pathways. These results implied that as a natural component of milk, lactotransferrin will has important application potential in the prevention and therapy of NPC and other EBV related diseases.