Background: Some of the severe diseases in the neonatal period lead to a myocardial injury that, if not detected promptly, would affect prognosis. Detection of acquired myocardial injury in the early stages of the diseases may be possible with simultaneous examination by echocardiography and determination of serum troponin I levels. Methods: In this cross-sectional study, between December 2016 and December 2018, myocardial function of 60 (33 males, 27 females) term neonates with a mean birth weight 3175.5 ± 441.18 grams who were at least 72 hours under ventilation, was studied using conventional and tissue Doppler echocardiography and measuring serum troponin I levels by ELFA method. Results: Mean and standard deviation of serum troponin I level, left and right MPI in neonates under study were 0.22 ± 0.64, 40.11 ± 0.11, and 0.41 ± 0.13, respectively. The correlation coefficient between serum troponin I level related to right MPI was +0.502 (P < 0.001) and left myocardial performance index was +0.524 (P < 0.001), and other criteria correlated to troponin I on right side of heart were Em, Sm, TAPSE, TR gradient in patients with PH was related to troponin I levels (P < 0.001). Conclusions: Serum level of troponin I is helpful in determination of right and left myocardial dysfunction especially in the presence of pulmonary hypertension in the neonates under mechanical ventilation.