Calcifying odontogenic cysts (COCs) represent a group of rare odontogenic lesions with a diversity of clinicopathological and behavioral features. According to the WHO classification of head and neck tumors in 2005, COC has been divided into calcifying cystic odontogenic tumor (CCOT), dentinogenic ghost cell tumor (DGCT) and ghost cell odontogenic carcinoma (GCOC). With few reports available on its immunohistochemical profile, this study investigated the histopathological features and the expression of nuclear factor kappaB (NF-kappaB), Ki-67 and matrix metalloproteinase-9 (MMP-9) in CCOT, DGCT and GCOC. According to the WHO classification of head and neck tumors in 2005, 26 cases of the so-called COC were diagnosed as CCOT (n=14), DGCT (n=7) and GCOC (n=5), respectively. The specimens of 26 COCs and 10 classic ameloblastomas (as control group) were examined by immunohistochemistry using anti-NF-kappaB p65, anti-Ki-67 and anti-MMP-9 antibodies and by in situ hybridization(ISH)using anti-MMP-9 mRNA probes. Immunohistochemical reactivity for NF-kappaB was mainly detected in the cytoplasm of tumor cells, and nuclear reactivity was only seen in few tumor cells in COC and classic ameloblastomas. Rate of nuclear staining was less than 1%. The expression of Ki-67 in GCOC was significantly higher than those in CCOT (p<0.001), DGCT and ameloblastoma (p<0.005). In COCs and ameloblastomas, expression of MMP-9 mRNA and protein was detected in tumor cells as well as in stromal cells. The positive staining for MMP-9 protein was detected in stromal cells of all GCOC cases and was significantly stronger than those in CCOT and DGCT groups (p<0.05). NF-kappaB may minimally affect the progression and local invasiveness of CCOT, DGCT and GCOC. GCOC show significantly higher proliferative activity than CCOT and DGCT. MMP-9 in stroma is associated with invasive ability of the CCOT, DGCT and GCOC.