BACKGROUND: Congenital cytomegalovirus (cCMV) infection leads to a significant burden on the health system. Relevant insights have been reached in the understanding of primary infection (PI) during pregnancy. However, knowledge gaps still exist related to maternal non-primary infections (NPI). Severe neurologic damage and hearing loss are the possible outcomes in the 17-20% of affected children. Furthermore, neither risk prevention strategies nor management are currently available for these NPI patients. CASE PRESENTATION: We report on a male term newborn showing in the first days of life hyperexcitability, tremors and increased muscular tone, in addition to thrombocytopenia, initially related to an early-onset sepsis. Obstetric history revealed that the mother underwent steroid treatment during the whole first trimester of pregnancy. She had positive CMV IgG and negative CMV IgM antibodies throughout gestation. At 15 days of age, due to the persistence of neurological and hematological signs and abnormalities found on brain ultrasound (bilateral ventriculomegaly, and an anechoic lesion within the right caudothalamic grove at first related with grade I intraventricular hemorrhage) a brain magnetic resonance imaging (MRI) was performed, showing significant lesions highly suggestive of cCMV. Although such diagnostic hypothesis was unsuspected (in light of the association of clinical manifestations with perinatal sepsis and the misleading maternal serology), however CMV DNA detection on blood and urine was carried out, giving positive results in both samples for connatal infection diagnosis. Newborn CMV IgG and IgM antibodies resulted positive, while the IgG avidity test showed high values according to a likely early intrauterine infection. The antiviral therapy was therefore begun and continued for 6 months. He currently is 6 months old and included in a multidisciplinary follow-up. His growth is within the normal limits, but a neuromotor delay is present. Audiological and ophthalmological evaluations, laboratory as well as multiorgan ultrasound (US) examinations have not revealed further anomalies to date. CONCLUSIONS: Our case underlines that CMV reactivations or reinfections may be responsible, as well as PI, for significant and harmful effects on the fetus and newborn. It also shows the limited diagnostic and preventive/therapeutical weapons available against NPI during gestation. The present experience confirmed, indeed, the literature regarding the absence of valid laboratory test to identify women with preexisting immunity at risk of giving birth to an infected neonate. Women with previous immunity should be treated with precautionary protocols, including US monitoring and fetal MRI aimed at detecting cCMV. Brain MRI findings may be a pre-warning for newborns of mothers with previous immunity showing neurological symptoms and ultrasound abnormalities. In these cases, its execution may allow the identification of pathognomonic lesions.