To measure the prevalence of cytomegalovirus (CMV) infection in ectopic pregnancy (EP) and its effect on the expression of inducible and endothelial nitric oxide synthases (iNOS, eNOS) by Fallopian tubes (FT) bearing an EP. This was a prospective case-control study. Blood and tubal samples were collected from 84 Eps and 51 controls (20 total abdominal hysterectomy (TAH) during the luteal phase and another 31 tubal ligations). CMV IgM and IgG antibodies were measured by ELISA, and an IVD CE PCR kit was used to detect CMV in the FTs. iNOS and eNOS were measured by immunohistochemistry and quantitative RT-PCR in FTs obtained from CMV-positive EP (n = 12), and the results were compared with those obtained from CMV-negative EP (n = 11) and TAH (n = 8). The frequencies of CMV IgM (51.2 % vs 17.6 %), IgG (77.4 % vs 52.9 %) or both antibodies (41.6 % vs 11.7 %) were significantly higher in EP compared with control. CMV was more common by PCR in FTs from EP (21.4 %) than controls (5.9 %). Twelve women from the PCR positive EP cases (66.6 %) were also simultaneously positive for both CMV IgM & IgG antibodies and had higher expression of eNOS and iNOS at the protein and gene levels compared with negative EP and TAH. Tubal infection with CMV may lead to EP by increasing the production of endothelial and inducible NOS by the FT epithelial cells. Further studies are required to illustrate the role of CMV in the pathogenesis of EP.