Mucinous cystic neoplasms (MCNs) of the pancreas, ovary and lung have a similar histologic appearance. We investigated if immunohistochemical (IHC) studies could help in separating these neoplasms. Twenty-six ovarian MCNs (invasive carcinoma and borderline tumor), 12 pancreatic MCNs (invasive carcinoma, and with moderate or high-grade dysplasia), and 3 pulmonary MCNs (only invasive carcinoma) were retrieved. Our study demonstrated that pancreatic MCNs are positive for CDX-2 (67%), PDX-1 (100%), CK7 (83%) and CK20 (100%), while are negative for CA-125. The IHC profile of ovarian intestinal type MCN is similar to that of pancreatic MCNs, except for lower frequency of CDX-2 expression (29% vs. 67%). Ovarian endocervical like MCNs are positive for CA-125 (100%) and CK7 (100%), while are negative for CDX-2, PDX-1 and CK20. Pulmonary MCNs are positive for CDX-2 (100%), CK7 (100%) and CK20 (100%), while are negative for PDX-1 and CA-125. All tumors are negative for TTF-1, D2-40 and WT-1. We concluded that an IHC panel of CDX-2, PDX-1, CA-125, and CK20 is useful in separating MCNs of the pancreas, ovary and lung.