Chronic medical conditions can complicate maternal and fetal health during pregnancy, making unintended or mistimed pregnancy problematic. The use of highly effective reversible contraceptives is important for women with health issues, yet sometimes those same illnesses make the contraceptives themselves less effective or less safe. We review the evidence surrounding contraceptive use by women with six common medical conditions: systemic lupus erythematosus, diabetes mellitus, anticonvulsant use for epilepsy or mood disorder, HIV infection, migraine headache, and obesity. In some instances it is not possible to make a risk-free contraceptive choice, yet pregnancy may be even riskier. Good clinical judgment and patient counseling must be exercised.