We evaluated cytomegalovirus (CMV) immunoglobulin M (IgM) titer in pregnant women with primary infection as a predictive factor for congenital infection. Maternal CMV antibody screening during the first trimester was conducted prospectively at 16 centers in Japan between September 2013 and 2015. Women with confirmed maternal primary infection underwent testing for fetal congenital infection, and we investigated the positive predictive value of CMV IgM titer levels for congenital infection in women with a low IgG avidity. We identified 6 (8.6%) cases of congenital infection among 70 pregnant women with positive/borderline IgG, positive IgM and IgG avidity index ⩽35.0% and 11 (39.3%) among 28 women with IgG and/or IgM seroconversion. IgM titer level ⩾6.00 index showed the highest positive predictive value (17.1%). High titer of CMV IgM during the first trimester in pregnant women with primary infection is a risk factor for congenital infection.