Increased survival of children with juvenile systemic lupus erythematosus (jSLE) and improved prognosis have led to a change in the long-term health issues arising for jSLE patients. Preservation of gonadal functioning and fertility are of increasing importance for young adults with jSLE. Events during childhood, such as exposure to alkylating agents, may compromise the reproductive potential. Even in the absence of gonadotoxic therapies, fertility may be decreased through organs specific involvement with jSLE. Strategies to preserve the reproductive potential of girl and boys with jSLE are discussed.