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The aim of the study was to assess the use of echocardiographic measurements in newborns of diabetic mothers. Maternal diabetes is associated with an increased risk of morbidity and mortality in pregnancy and in perinatal period. Thirty-five newborns of diabetic mothers (pre- gestational or gestational diabetes; case group) and thirty-five controls (control group), born between January 2009 and December 2012 in Cluj-Napoca (north-west of Romania), were included in this study. A Logiq e ultrasound with an 8 MHz transducer was used to measure echocardiographic parameters. The interventricular septal thickness in case group was higher as compared with control group (at end systole = 6.61 ± 1.64 mm vs. 5.75 ± 0.95 mm, p = 0.0371; at end diastole = 4.61 ± 1.59 mm vs. 3.42 ± 0.70 mm, p = 0.0001). A risk ratio of 2.333 (0.656, 8.298) was obtained for septal hypertrophy. A higher proportion of septal hypertrophy was identified in the newborns of mothers with gestational diabetes compared to the newborns of pregestational diabetes mothers (p = 0.0058). The mean birth weight was significantly higher in newborns of diabetic mothers (3695.57 ± 738.63) as compared with controls (3276.14 ± 496.51; p = 0.0071). Infants born to mothers with diabetes proved to be at a high risk of septal hypertrophy.