We are pleased to bring you this supplement to Nephrology, which contains the proceedings of the 20th and 21st Japanese Clinicopathological Conference on Renal Allograft Pathology, held on 16 July 2016 in Tokyo and on 15 July 2017 in Nagoya, Japan, respectively. The conference is held annually, with clinical nephrologists, transplant surgeons, urologists and renal pathologists meeting to discuss the issues in cases and topics concerning renal transplantation. The conference has made a great contribution to the field of renal transplantation in Japan. Each year, we set several topics for detailed discussion at the conference. In 2016, the 20th conference consisted of one educational lecture, two special lectures, 18 oral presentations and 15 poster presentations, which focused on graft dysfunction in the chronic phase, recurrent kidney disease and infection. The educational lecture titled ‘Post-transplant immunoglobulin A deposition and nephropathy in allografts’ was presented by Dr. Tadashi Sofue and is published in this supplement. Mr. Shigeru Horita discussed ‘Usefulness of immunofluorescence technique in transplant kidney biopsy’ in one of the special lectures, and the other, ‘Essence of the Banff 2015 meeting’, was delivered by Dr. Sigeo Hara. In 2017, the 21st conference comprised two educational lectures, two special lectures, 15 oral presentations and eight poster presentations. An overview of the educational lecture ‘Recurrence of native kidney disease after kidney transplantation’, which was presented by Dr. Izumi Yamamoto, is published in this supplement. Also, Professor Ken Sakai spoke about ‘Protocol graft biopsy in kidney transplantation’. The special lecture titled ‘Viral infections directly involve in kidney allograft function’ was presented by Dr. Kosuke Masutani, and is published in this supplement as a mini review. In addition, Dr. Shigeo Hara discussed ‘Cell-mediated rejection revisited: past, current, and future direction’. We believe that the reports in this supplement address recent important issues in the field of renal transplantation. The guest editors thank all authors and participants for their contributions. Finally, we would like to express our sincere appreciation to Dr. Morozumi and Dr. Yamaguchi for their dedication to these conferences. The authors have no conflicts of interest to declare.