Percutaneous lithotomy is the gold standard in the treatment of large kidney stones. Several steps of the operation might cause severe complications. Safe procedures depend on careful planning, accurate performance, recognition of problems and knowledge of how to handle them. Relevant steps of percutaneous stone treatment with possible complications and their management are presented. Current topics in percutaneous stone treatment taking into consideration the relevant literature are discussed. Furthermore, rare complications and strategies for safe management are presented. Careful planning and adequate preoperative diagnostic workup are essential for safe procedures. Puncture of the renal calyceal system and tract dilation might lead to severe complications. Bleeding and infectious complications are the most common problems. Availability of interventional radiology provides ideal emergency treatment in case of severe bleeding and helps to avoid surgical revision with high risk of organ loss. Percutaneous stone treatment is a safe and effective therapy in an experienced physician's hands. Careful planning and accurate performance help to avoid severe complications.