<b><i>Background:</i></b> Cortical bone is a significant determinant of bone strength and its deterioration contributes to bone fragility. Thin cortices and increased cortical porosity have been noted in patients with chronic kidney disease (CKD), but the “Turnover Mineralization Volume” classification of renal osteodystrophy does not emphasize cortical bone as a key parameter. We aimed to assess trabecular and cortical bone microarchitecture by histomorphometry and micro-CT in patients with CKD G5 and 5D (dialysis). <b><i>Methods:</i></b> Transiliac bone biopsies were performed in 14 patients undergoing kidney transplantation (<i>n</i> = 12) and parathyroidectomy (<i>n</i> = 2). Structural parameters were analysed by histomorphometry and micro-CT including trabecular bone volume, thickness (TbTh), number (TbN) and separation and cortical thickness (CtTh) and porosity (CtPo). Indices of bone remodelling and mineralisation were obtained and relationships to bone biomarkers examined. Associations were determined by Spearman’s or Pearson’s rank correlation coefficients. <b><i>Results:</i></b> By micro-CT, trabecular parameters were within normal ranges in most patients, but all patients showed very low CtTh (127 ± 44 µm) and high CtPo (60.3 ± 22.5%). CtPo was inversely related to TbN (<i>r</i> = –0.56; <i>p</i> = 0.03) by micro-CT and to TbTh (<i>r</i> = –0.60; <i>p</i> = 0.024) by histomorphometry and correlated to parathyroid hormone values (<i>r </i>= 0.62; <i>p</i> = 0.021). By histomorphometry, bone turnover was high in 50%, low in 21% and normal in 29%, while 36% showed abnormal patterns of mineralization. Significant positive associations were observed between osteoblast surface, osteoclast surface, mineralization surface and bone turnover markers. <b><i>Conclusions:</i></b> Deterioration of cortical ­microarchitecture despite predominantly normal trabecular parameters reinforces the importance of comprehensive cortical evaluation in patients with CKD.