The aim of this study is to evaluate the changes in myocardial functions in children who underwent haematopoietic stem cell transplantation along with associated chemotherapy. Additionally, we evaluated the effect of baseline echocardiographic parameters on mortality. We evaluated 39 patients (mean age 7.4 years) who underwent haematopoietic stem cell transplantation owing to non-malignant disease. The control group included 39 healthy children who had normal cardiac findings. The myocardial functions were evaluated in all subjects by conventional echocardiography and tissue Doppler echocardiography before haematopoietic stem cell transplantation and in the 1st, 3rd, 6th, and 12th month after haematopoietic stem cell transplantation. All patients had normal left ventricular ejection fraction before haematopoietic stem cell transplantation, except one case. Before haematopoietic stem cell transplantation, the patient group had significantly greater mean pulmonary artery pressure and lower tricuspid valve annular plane excursion rate. Baseline E’ velocities for mitral lateral annuli, septum, and tricuspid lateral annuli were lower in the patient group than the control group. The E’ velocities for the left ventricle decreased in the patient group after haematopoietic stem cell transplantation, and then returned to baseline levels at the 6 months. E’ and S’ velocities for tricuspid lateral annuli also decreased after haematopoietic stem cell transplantation and were still depressed in the first year after haematopoietic stem cell transplantation. Baseline E’ velocity for septum was significantly lower in patients who died after haematopoietic stem cell transplantation than patients who survived (p = 0.009). Subclinical impairment in both ventricular functions was observed after haematopoietic stem cell transplantation and the right ventricular functions were affected for longer periods than left ventricle after haematopoietic stem cell transplantation. The myocardial functions should be monitored after the first year of haematopoietic stem cell transplantation.