Introduction. Cytomegaly is an infectious, widespread viral disease. It is caused by Cytomegalovirus (CMV), which belongs to the DNA viruses group from the Herpesviridae family. The virus is human specific. Once infected, a person remains seropositive to the end of life and the virus remains latent particularly in leukocytes, which are its main reservoir. Many different disease manifestations, which depend partially on a patient’s age, but mostly on an immunological state, may be caused by CMV. Aim. The aim of this work was the assessment and histoclinical analysis of CMV infection in a male newborn with a congenital anomaly syndrome. Case study and examination results. A male newborn, born in the 30th week of gestation, diagnosed with congenital anomaly syndrome, Apgar score was 2. In the neonatal period hypertrophic cardiomyopathy involving the right ventricle, esophageal atresion, esophagotracheal fistula, hepatosplenomegaly, respiratory insufficiency and hyperechogenic periventricular structures in the brain were diagnosed. During the entire hospitalization period a progression of inflammatory changes in the lungs was observed. The results of serological tests to detect anti-CMV and toxoplasmosis specific antibodies were: CMV–IgG 21.00 IU/mL; CMV–IgM negative; Toxo–IgG 4.0 IU/mL; Toxo–IgM negative. Restoration of esophageal continuity and repair of the fistula were performed surgically. Follow-u p serological test was positive for anti-CMV antibodies in the IgG and IgM classes. The patient died on the 79th day following hospital admission. Autopsy and histopathological tests confirmed generalized cytomegalovirus infection. Discussion. Most advanced histopathological changes were observed in lungs, liver, spleen and brain. Characteristically changed cells, confirming generalized cytomegalovirus infection were found in all the aforementioned organs. Conclusions. CMV infections, particularly congenital infections in premature newborns are challenging diagnostic and therapeutic problems. Routine diagnostic procedures to detect CMV infections seem to be necessary in risk groups, particularly for premature infants. Negative anti-CMV antibodies result in patients with an insufficient immune system, does not exclude the presence of this infection. Early diagnosis and treatment of congenital cytomegaly may positively affect a patient’s clinical condition and prolonged prognosis.