Myeloablative conditioning regimens with significant extramedullary toxicity result in high rates of renal dysfunction including acute kidney injury (AKI). Here we examine the incidence and impact of a reduced creatinine clearance (below 60 ml/min) before day 90 (early renal dysfunction, ERD) in patients receiving the reduced toxicity fludarabine/i.v. busulfan (FluBu4) regimen prior to allogeneic transplant. Of 91 patients receiving FluBu4, 62 (68%) developed ERD. ERD resulted in worse overall survival (OS, 2.2 years versus median not reached, p = 0.04) and progression-free survival (PFS, 1.6 years versus median not reached, p = 0.02). This was due to a higher relapse rate (34% versus 14%, p = 0.03) in the ERD group. In time-dependent Cox proportional hazards models adjusted for age, ERD was associated with worse OS (hazard ratio [HR] 2.67, 95% confidence interval [CI] 1.06-4.21, p = 0.043) and PFS (HR 2.52, 95% CI 1.17-4.28, p = 0.030). Patients with ERD surviving 1 year had an increased risk of chronic kidney disease (CKD, OR 10; 95% CI 1.4-112.6, p = 0.0181), which was associated with worse survival (3.2 years versus median not reached, p = 0.002). ERD after FluBu4 is therefore a poor prognostic sign resulting in increased relapse, worse OS, and high risk of CKD at 1 year.