Mannose-binding lectin (MBL) gene polymorphisms may be associated with adult-onset systemic lupus erythematosus (SLE), but studies in children with SLE are rare. This study tested the genetic association between MBL polymorphisms and paediatric-onset SLE in a cohort of Chinese children in Taiwan. In all 150 children with SLE and 100 healthy controls of comparable age were genotyped for codon 52, 54 and 57 mutations of the MBL gene using a polymerase chain reaction-based assay. Clinical manifestations, organ involvement, disease activity, laboratory characteristics and outcome were recorded and compared between patients with different MBL genotypes. Codon 54 mutation was fairly common in both SLE patients and controls, whereas codon 52 and codon 57 mutations were not detected in our study subjects. No statistically significant differences were found in allele frequencies of the codon 54 mutation between SLE and control groups. Moreover, no association was found between this MBL polymorphism and clinical manifestations, organ involvement, disease activity, laboratory characteristics or outcome of SLE. These results suggest that MBL polymorphisms do not influence susceptibility to paediatric-onset SLE and do not influence clinical manifestations of SLE in Chinese children.