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Background: Hepatitis E Virus (HEV) is a major public health problem in developing countries and often fatal among pregnant women in the third trimester. Objectives: The study investigated the sero-prevalence and risk factors of HEV infection among pregnant women attendee of University of Maiduguri Teaching Hospital, Maiduguri, Nigeria. Methods: The cross-sectional study was carried out between 4th January 2016 to 30th May, 2016. One hundred and eighty blood samples from pregnant women who consented and enrolled for the study were analyzed for anti – HEV IgM using a quality assured commercial Enzyme Linked Immunosorbent Assay (ELISA) kit. Structured questionnaires were used to collate the sociodemographic characteristics and risk factor of study subjects. Results: Out of the 180 pregnant women sampled, the anti-HEV IgM seroprevalence of 13.3% was recorded. The seroprevalence was significantly higher in the age range of 31 – 35 years (26.5%) and least in age range ≤ 20 years (4.9%) (p=0.009). The highest seroprevalence was recorded in the third trimester 14.1% followed by second (p>0.05). After logistic regression, nature of toilet system, and source of water consumption were significant risk factors for active HEV infection (p˂0.05). Conclusion: Based on the 10.8 % pooled national prevalence of HEV infection in Nigeria, this study recorded a significantly high level of anti – HEV IgM seropositivity, an indication of recent and active HEV infection among pregnant women at the study area. Also, these infections are most among the pregnant women in their third trimester. HEV infection was related to personal, water and environmental hygiene.