Aim The goal of this study was to identify novel anti-endothelial non–HLA antibodies (Ab) associated with kidney allograft rejection and assess a panel of novel and previously discovered non–HLA Ab in a pediatric kidney allograft recipient cohort. Methods Endothelial cell cross matches (ECXM) were used to screen patients for non–HLA Ab associated with rejection. 16 of 279 kidney allograft recipients tested were positive for both ECXM and rejection. Post-transplant neat and EC eluted sera from these 16 ECXM + Rejection + patients, as well as available pre-transplant sera from these patients were analyzed by protein microarrays (ProtoArray, Thermo Fisher Scientific) to screen 9,000 human proteins and identify antigens bound by patient sera (Prospector software, z-score ⩾ 3 and CV 0.05). 12 novel non–HLA Ab identified by protein microarray and 67 previously published non-Ab targets identified in kidney (n = 27), heart (n = 31), lung (n = 8), and liver (n = 1) transplant were conjugated to multiplex bead arrays. This panel of non–HLA targets was validated in a longitudinal single center pediatric cohort (n = 65). Results Protein microarray analysis of the ECXM + Rejection + sera identified 391 proteins in the pre-transplant sera, 1252 proteins in the neat sera, and 388 proteins in the EC eluted sera. 135/388 eluted sera of ECXM + Rejection + EC specific proteins were newly detected in post-transplant sera. 12/135 novel Ab were prioritized to select for ligands with endothelial membrane localization, kidney expression and an increased Ab binding frequency. Rank sum analysis of a single-center pediatric kidney allograft recipient cohort (n = 65) identified peroxisomal-trans-2-enoyl-coA-reductase (p = 0.03) and a novel non–HLA Ab (p = 0.05) associated with rejection at the patient level. Conclusions Non–HLA antibodies are associated with an increased risk of allograft rejection emphasizing the importance of further identification and validation of non–HLA Ab in transplantation. Assessment of a panel of non–HLA Ab appears to be useful to elucidate the incidence and specificity of non–HLA Ab associated with kidney allograft rejection. B.L. Ray: 5. Employee; Company/Organization; Immucor, Inc. E.F. Reed: 1. Grant/Research Support; Company/Organization; Immucor, Inc.