Given the superior outcomes compared to dialysis, most children with end-stage kidney disease (ESKD) are currently referred for kidney transplantation. Kidney transplants are exposed to various types of injuries that occur as a result of hemodynamic disturbances, transplant rejection, infections, drug toxicity, metabolic disorders, and the recurrence of diseases originating in the native kidneys. Kidney allograft biopsy is the primary tool in the diagnostics of graft pathologies, enabling identification of lesions that may potentially be stopped or slowed down with proper treatment. The majority of kidney transplant histopathological images are not fully specific and therefore must be interpreted in context. In recent years, serological testing for the detection and monitoring of antibodies directed against transplant and non-transplant antigens in the graft, as well as molecular approaches aiming to trace changes that develop in the transplant based on fluctuations in gene expression have added to the pathology repertoire. The widening spectrum of tests and methods available has deepened our understanding of transplant pathology and also improved the accuracy of diagnosis.