Purpose Renal dysfunction is a well-known long-term complication which could increase mortality after non-renal solid organ transplantation. Recently, the UNCX variant (rs10277115), which encodes a paired-type homeobox transcription factor and has essential roles in skeleton formation and kidney development, has been shown to be associated with increased risk for chronic kidney disease in east Asian populations. However, the association between the UNCX variant and renal dysfunction after lung transplantation (LT) has not yet been elucidated. In the present study, we evaluated the association between the UNCX variant and the postoperative change of renal function after LT. Methods A total of 99 recipients of LT more than 18 years were genotyped for the functional polymorphism of the UNCX gene (rs10277115) and divided into two groups: the wild-type allele (AA) group and the heterozygous and homozygous mutant allele (AT/TT) group. The results of renal function tests were compared between the two groups. Delta creatinine (ΔCr) and delta eGFR (ΔeGFR) were defined as the difference between the postoperative level and the preoperative baseline level. Results The clinical characteristics of the patients were similar between the two groups. There were no significant differences in the previously described risk factors for renal function, including age, diabetes mellitus, hypertension and dyslipidemia. The postoperative change of ΔCr was significantly higher in the AA group than the AT/TT group after LT (Figure 1(a)). Moreover, the postoperative change of ΔeGFR was significantly lower in the AA group than the AT/TT group after LT (Figure 1(b)). The multivariate analysis revealed that the UNCX variant was independently associated with the levels of ΔCr and ΔeGFR. Conclusion The UNCX variant was associated with significant differences in Cr and eGFR in the long term and the development of renal dysfunction after LT.