Our aim was to determine whether the Fc receptor-like 3 (FCRL3) -169 C/T (rs7528684) polymorphism confers susceptibility to systemic lupus erythematosus (SLE). A meta-analysis was conducted on the associations between the FCRL3 -169 C/T polymorphism and the SLE. A total of nine sets of comparisons containing 3,628 patients and 6,490 controls were considered. The meta-analysis showed no association between the SLE and the FCRL3 -169 C allele in all study patients (odds ratio [OR] = 0.999, 95 % confidence interval [CI] = 0.925-1.080, p = 0.986). Stratification by ethnicity indicated no association between the C allele and the SLE in neither Europeans nor Asians (OR = 1.058, 95 % CI = 0.925-1.250, p = 0.414; OR = 0.981, 95 % CI = 0.884-1.088, p = 0.715). Furthermore, analysis using the recessive model, the dominant model, and the homozygote contrast showed the same pattern for the C allele in European and Asian groups, showing no association between the FCRL3 -169 C/T polymorphism and the SLE. Even after excluding studies whose controls were not in Hardy-Weinberg equilibrium, we found that this did not materially affect the meta-analysis results. However, the single Latin American study did show an association between the FCRL3 polymorphism and the SLE under homozygote contrast (OR for CC vs. TT = 2.689, 95 % CI = 1.152-1.277, p = 0.022). This meta-analysis of published studies including 2,544 patients and 3,913 controls demonstrates that the FCRL3 -169 C/T polymorphism does not confer susceptibility to SLE in Europeans or Asians.