Heart and/or lung transplantation are life-saving treatments for end-stage cardiopulmonary disease; however, chronic renal failure may develop. The impact of thoracic organ transplant on renal function in infants and children is not well characterized. This retrospective cohort study evaluated renal function following thoracic organ transplantation in 46 children (32 heart, 9 lung, 5 heart-lung; median age 4.1 years) with at least 12 months of follow-up. Glomerular filtration rate (GFR, ml/min/1.73 m2) was estimated by the Schwartz formula throughout and each GFR estimate was converted to per cent normal for age (GFR%). Changes in renal function following transplantation were analyzed using longitudinal mixed-effects linear regression models. GFR% decreased following thoracic organ transplantation (p <0.001). Younger age at transplant was associated with a greater decline in GFR% (p <0.01). The decline in GFR% persisted after adjustment for nutritional status with body mass index or weight-for-length z-scores. The prevalence of renal insufficiency (GFR% <75) increased from 22% at transplant to 55% and 85% at 1 and 5 years post transplant, respectively, while 15% had a GFR% <50 at 5 years post transplantation. Higher tacrolimus trough levels over the first 6 months correlated with a lower GFR% (p <0.01). Renal function declined significantly following thoracic organ transplantation.