The ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase (CD38) gene is a positional and functional candidate gene for the susceptibility to systemic lupus erythematosus (SLE) because CD38 gene maps in the described SLE risk region 4p15 and CD38 molecule is a leukocyte activation antigen and ectoenzyme involved in numerous immune functions. The aim of this study was to investigate the possible association of the polymorphisms located at positions 182 of intron 1 (C/G) and 418 (C/T, located in exon 3) of the CD38 gene with the susceptibility and clinical features of SLE. Genotyping of 276 Spanish patients with SLE and 194 controls was performed by polymerase chain reaction amplification-refractory mutation system techniques. No association between the polymorphisms studied and the susceptibility to SLE was found. However, when patients were stratified according to their clinical manifestations, a significant increase of CC individuals and a significant decrease of CG individuals among patients with discoid rash (67.9% vs. 53.1% in controls p = 0.02, pc > 0.05, odds ratio [OR] = 1.87, 95% confidence interval [95% CI] 1.05-3.35; and 23.5% vs. 40.2% in controls, p = 0.008, pc = 0.024, OR = 0.46 95% CI 0.24-0.85) were found. Logistic regression analysis identified CC genotype as an independent risk factor for discoid rash among patients with SLE (p = 0.01, OR = 2.23, 95% CI 1.19-4.18). In conclusion, a slight contribution of the polymorphism located in intron 1 of the CD38 gene in the clinical features of SLE could be postulated.