BackgroundMaternal cytomegalovirus (CMV) and Rubella infections result in adverse neonatal outcomes. Both CMV and Rubella are more widespread in developing countries and in communities with lower socioeconomic status. Thus, the aim of this study was to determine IgM specific to CMV and Rubella among newborns and Maternal CMV-seroprevalence and to identify risk factors.Method and findingUsing cross sectional study design a total of 312 (156 newborns and 156 mothers) study participants were recruited by simple random sampling technique from gynecology outpatient department (OPD) and ward, starting from April 1, 2015 to June 30, 2015. Cord and venous blood samples were collected from all participants and structured questionnaire was introduced to gather risk factor related data. ELISA was used to detect CMV and Rubella-IgM. SPSS version 20 was used to analyze the data, and regression analysis was also performed. Out of 156 newborns, 2 [1.3 %; 95 % CI: 0.0–3.8] were positive for CMV—IgM and no single rubella was detected. Association was not computed between risk related variables and cytomegalovirus infected newborns due to the low positivity rate. Multiple independent predictors were found between maternal CMV-IgM and Obstetrical characteristics. Cytomegalovirus—IgM was significantly isolated from mothers with history of transfusion (25.0 %, OR 0.09, 95 % CI 0.0–0.3, P = 0.006), history of abortion (OR 0.02, 95 % CI 0.0–0.6, P = 0.023), HIV sero-status (OR 5.0, 95 % CI 1.5–15.8, P = 0.034), and multi parity (OR 0.08, 95 % CI 0.01–0.7, P = 0.022).ConclusionAlthough low congenital CMV and no Rubella are reported among newborns, more effort is needed to screen for congenital infectious viral disease as well as usage of advanced techniques should be taken into consideration.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-016-2274-1) contains supplementary material, which is available to authorized users.