Cortical bone represents nearly 80 % of human bone mass and is the major determinant of bone strength; however, cortical bone parameters and their relationship to trabecular bone in the pediatric chronic kidney disease (CKD) population have not been evaluated. Biochemical values and cortical and trabecular bone parameters were assessed in 22 pediatric dialysis patients: 12 with high and 10 with normal to low trabecular bone turnover. Trabecular bone turnover and osteoid volume correlated with parathyroid hormone (PTH) levels (r = 0.86, p < 0.01 and r = 0.93, p < 0.01, respectively). Internal cortical osteonal bone formation rate was directly related to alkaline phosphatase (r = 0.45, p < 0.05) and inversely related to insulin-like growth factor (IGF)-1 values (r = -0.55, p < 0.01), and internal cortical porosity was also related to serum alkaline phosphatase levels (r = 0.57, p < 0.01). A similar relationship was not found between external cortical bone formation rate and parameters of bone turnover and porosity, however. No relationship was found between trabecular and cortical bone formation rates. Secondary hyperparathyroidism was associated with increased external cortical, relative to internal cortical, osteonal activity in pediatric dialysis patients. The clinical consequences of these changes and their response to therapy for secondary hyperparathyroidism remain to be defined.