We describe a case of collapsing focal segmental glomerulosclerosis and severe kidney dysfunction in a liver transplant recipient after the initiation of alendronate for osteopenia. In view of the increasing incidence of chronic kidney disease in long-term liver transplant patients, bisphosphonates need to be used with caution in these patients. The usefulness of bisphosphonates for the prevention of early bone loss after liver transplantation is increasingly reported. However, there is little information on the safety and efficacy of these drugs when used in the later stages of liver transplant, particularly in the presence of chronic kidney disease. Bisphosphonates are excreted unchanged via the kidneys after reaching the systemic circulation. Some cases of severe kidney injury, in particular collapsing focal segmental glomerulosclerosis, have been described that are associated with the use of pamidronate. Alendronate, a widely used bisphosphonate in transplant patients, has not been related to kidney toxicity. We describe a case of collapsing focal segmental glomerulosclerosis and severe kidney dysfunction in a liver transplant recipient soon after the initiation of alendronate for osteopenia. Possible pathogenetic mechanisms are discussed. In view of the increasing incidence of chronic kidney disease in long-term liver transplant patients, bisphosphonate need to be used with caution in patients with a low glomerular filtration rate.