We aimed to study the incidence, predictors and outcome of chronic kidney disease (CKD) after heart transplantation (HT). All our HT patients 1988–2010 were considered for inclusion. Of these, 134 came for annual follow-ups including evaluation of glomerular filtration rate (GFR) using iohexol clearance measurements, and the CKD-EPI (adults) or Schwartz (children) formulae. Median GFR (Q1–Q3) (ml/min/1.73 m2) declined from 67.0 (50.0–82.0) during transplant assessment (TA) to 56.0 (45.0–69.0) at year 1, 53.0 (41.0–68.0) at year 5 and 44.5 (25.0–57.3) at year 10. The cumulative incidence of CKD ≥ stage 4 was 25% at 5 years and 41% at 10 years after transplantation. Proteinuria the first year post-HT was the only predictor related (P < 0.05) to a higher rate of GFR decline (HR 5.15, 95% CI 1.23–21.55). GFR ≥60 as compared to <60 before HT, or a first-year GFR decline <30% as compared to >30%, was moreover associated (P < 0.05) with a lower risk of death (HR 0.30, 95% CI 0.12–0.76 and HR 0.35, 95% CI 0.13–0.90, respectively). Notably, the CKD-EPI and Schwartz formulae overestimated GFR by 28 ± 29% and 26 ± 33%, respectively. In conclusion, CKD in HT patients is common and associated with worse outcome. To avoid diagnostic delay, GFR estimating equations' validity in HT patients needs further study.