The risk factors associated with CMV DNAemia are not well known after haploidentical stem cell transplantation (SCT).This study investigated the risk factors and prognosis for CMV DNAemia among CMV seromatched donors and recipients (D+/R+).A retrospective study of patients undergoing haploidentical stem cell transplantation (SCT) between January 2010 and January 2012 was conducted. Cox regression analysis was performed to identify the risk factors for CMV DNAemia. These possible factors included recipient/donor age, recipient/donor gender, gender disparity, recipient HBsAg serostatus, diagnosis, risk stratification, anti-thymocyte globulin (ATG) dose (6 mg/kg,10 mg/kg), early neutrophil engraftment (≤12 days, >12 days), absolute lymphocyte count on day 30 (ALC30) and the occurrence of acute GVHD before CMV DNAemia.The total number of patients was 248 with median age of 31 years (range, 14–56). The cumulative incidence of CMV DNAemia (146/248) was 59.5%. CMV DNAemia was first detected after a median of +35 days (range,12–82). Seventeen patients (17/146, 11.6%) developed CMV disease. Multivariate analysis identified HBsAg seropositivity (P = 0.002, hazard ratio (HR) = 1.833; 95%CI = 1.257–2.673) and the occurrence of acute GVHD before CMV DNAemia (P = 0.014; HR = 1.520; 95%CI = 1.088–2.124) as risk factors for CMV DNAemia. CMV DNAemia was associated with subsequent II-IV acute graft-versus-host disease (GVHD) (P = 0.014), III-IV aGVHD (P = 0.013) and chronic GVHD (P = 0.008). Totally, CMV DNAemia was found to be a poor prognostic factor in terms of non-relapse mortality (NRM) (P = 0.003, HR = 2.730; 95%CI = 1.406–5.197), and overall survival (OS) (P = 0.045, HR = 1.654; 95%CI = 1.012–2.701).Our data showed HBsAg seropositivity was associated with an increased risk of cytomegalovirus DNAemia. Detection of CMV DNAemia proved to be a poor prognostic factor for haploidentical patients.