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To analyze the association of the PD‐1.3 polymorphism within the PDCD1 gene in patients with systemic lupus erythematosus (SLE) from the homogeneous population in northern Sweden. The PD‐1.3A allele was analyzed in relation to disease manifestations and severity representing various phenotypes of SLE.The study group comprised 260 patients fulfilling at least 4 of the American College of Rheumatology (ACR) criteria for SLE during 1 year. The Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) and the Systemic Lupus International Collaborating Clinics/ACR damage index scores were recorded. Population‐based, randomly selected individuals (n = 670) from the same geographic area served as controls. DNA was extracted from blood samples from both patients and controls and was genotyped for the PD‐1.3 A/G polymorphism, using an ABI Prism 7900HT Sequence Detection System.The frequency distribution of alleles, carriers, or genotypes did not differ between patients and controls. The PD‐1.3A allele and carriage of the A allele were highly associated with renal disorder (ACR criterion 7) (P = 0.005, odds ratio [OR] 2.71 [95% confidence interval (95% CI) 1.32–5.55] and P = 0.012, OR 2.62 [95% CI 1.28–5.35], respectively). In regression analysis adjusted for sex and age at disease onset, carriage of the A allele remained significantly associated with renal disorder (P = 0.002, OR 3.54 [95% CI 1.56–8.01]). The presence of proteinuria, as measured by the SLEDAI score, and the presence of renal damage were also significantly associated with carriage of the A allele (P = 0.007, OR 3.88 [95% CI 1.44–10.47] and P = 0.021, OR 2.98 [95% CI 1.18–7.54], respectively).The PD‐1.3A allele is associated with renal manifestations in SLE patients from northern Sweden but not with susceptibility to SLE per se. [ABSTRACT FROM AUTHOR]