Children with chronic kidney disease suffer from excessive cardiovascular mortality and early alterations of the cardiovascular system. Tissue doppler imaging is a validated echocardiographic tool to assess early systolic and diastolic cardiac dysfunction. We hypothesized that tissue Doppler velocities would reveal reduced cardiac function in children with chronic kidney disease compared to healthy children. A standardized echocardiographic exam was performed in 128 patients of the Cardiovascular Comorbidity in Children with Chronic Kidney Disease (4C) Study aged 6–17 years with an estimated glomerular filtration rate (eGFR) below 60 ml/min/1.73 m2. Tissue Doppler measurements included early (E’) and late (A’) diastolic and systolic (S’) velocity at the mitral and septal annulus of the left ventricle. Measured values were normalized to z-scores using published reference data. Predictors of E’/A’, E/E’, S’ and left ventricular mass index (LVMI) were assessed by multiple linear regression analyses. Tissue Doppler E’ was reduced and tissue Doppler A’ increased, resulting in a reduced tissue Doppler E’/A’ ratio (z-score −0.14, p <0.0001) indicating reduced diastolic function compared to healthy children. Reduced tissue Doppler E’/A’ Z-Scores were independently associated with lower eGFR (p = 0.002) and increased systolic blood pressure (p = 0.02). While E/E’ Z-Scores were increased (Z-score 0.57, p <0.0001), patients treated with pharmacological RAS blockade but not with other antihypertensive treatments had significantly lower E/E’ and higher E’/A’ Z-Scores. Systolic tissue Doppler velocities were significantly decreased (Z-score −0.24, p = 0.001) and inversely correlated with E/E’ Z-Scores (r = −0.41, p <0.0001). LVMI was not associated with systolic or diastolic tissue Doppler velocities. Concentric left ventricular hypertrophy showed a tendency to lower S’ in multivariate analysis (p = 0.13) but no association to diastolic function. Concentric left ventricular geometry was significantly associated with lower midwall fractional shortening. In summary, systolic and diastolic function assessed by tissue Doppler is impaired. eGFR, systolic blood pressure and the type of antihypertensive medications are significant predictors of diastolic function in children with CKD. Left ventricular morphology is largely independent of tissue Doppler velocities. Tissue Doppler velocities provide sensitive information about early left ventricular dysfunction in this population.