Congenital disorders are a leading cause of global burden of disease; the birth prevalence remains constant at 6%. Initiating preconception care before pregnancy may be an effective strategy to reduce congenital disorders and improve the health of reproductive-age women. Our objectives are: (1) To identify components of preconception interventions, (2) to assess the effectiveness of preconception interventions in reducing the burden of congenital disorders, and (3) to prioritize these interventions. Medline and Science Direct search terms included: preconception, pre-pregnancy, childbearing, reproduction, care, intervention, primary care, healthcare, model, program, prevention, trial, efficacy, effectiveness, congenital disorders OR abnormalities. Inclusion criteria were: (1) English, (2) human subjects, (3) women of childbearing age, (4) 1980-current data, (5) all countries, (6) experimental studies, (7) systematic reviews or meta-analysis, (8) program reports/evaluations. Data was collected and abstracted by two independent reviewers. To prioritize preconception interventions likely to have the largest impact at a population level, a ranked scoring system was created incorporating the following: (1) quality of evidence supporting the intervention, (2) effect size of the intervention, and (3) global burden of the specific congenital disease. Preconception interventions include risk screening, education, motivational counseling, disease optimization and specialist referral. The most effective interventions, based on the strength of evidence, size of impact of intervention, and disease burden are: folic acid fortification/supplementation, diabetic control, smoking and alcohol interventions, HIV management, thrombophillia screening, obesity prevention and epilepsy management. Although multiple conditions require preconception attention, only nine interventions have evidence to support their effect on congenital disorders through a randomised control trial, systematic review or meta-analysis. There is a need for more high-level research in evaluating certain preconception interventions. These findings have significant implications on planning and implementation of preconception care.