Children with chronic kidney disease (CKD) are at high risk of developing impaired bone quality. Our aim was to investigate changes of bone quality in children with CKD in relation to their treatmant using two imaging techniques-dual energy X-ray absorptiometry and quantitative ultraSonography (QUS). Thirty-three patients with CKD (18 boys and 15 girls, mean age 10.37 ± 3.37 years) were evaluated with bone mineral density (BMD) measured by DXA at the lumbar spine and hip and with speed of sound (SOS) measured by QUS at the radius and tibia at the beginning and at the end of the study. The patient cohort consisted of 14 patients with CKD stage 3-4 not treated with dialysis (CKD group), 5 patients on peritoneal dialysis treatment (PD group) and 14 patients after kidney transplantation (RTx group). BMD measurements did not show any significant changes in CKD and PD patients during the study. There was a reduction in BMD measured at the lumbar spine, femoral neck and total hip in RTx patients that was approaching significance. During the 2-year follow-up, SOS measurements at the radius decreased significantly in PD patients, whereas SOS measurements at the tibia significantly improved in RTx patients. No significant changes in QUS parameters were recorded for patients in the CKD group. In conclusion, our study shows that QUS parameters seem to better reflect the state of hyperparathyroidism of renal osteodystrophy as they deteriorate significantly in patients on dialysis and improve after renal transplantation.