Chronic allograft nephropathy includes chronic calcineurin nephrotoxicity, recurrent and de novo glomerulonephritis and a group of disorders with graft dysfunction of unknown etiology designated chronic rejection. Review of risk factors of the latter category show that the chronic rejection lesions emerge in organs that have undergone injury. Despite the relevance of nonalloantigen-dependent progression factors in the tissue injury, alloantigen-dependent factors predominate in the pathogenesis. Lately, B cell responses have received increasing interest in transplant rejection and include responses against both major histocompatibility complex (MHC) and tissue-specific antigens, mainly on the endothelium and in the glomeruli. These humoral responses are thought to be involved in the development of vascular and glomerular lesions. Furthermore, at the tissue level, markers of senescence are found in the tubular epithelium contributing to the lesions of tubular atrophy and interstitial fibrosis.