Homelessness during pregnancy poses significant health risks for mothers and infants. As health care providers increase their emphasis on social determinants of health, it is important to understand how unstable housing contributes to complications during pregnancy. We linked data about emergency shelter enrollees with Massachusetts Medicaid claims for the period January 1, 2008-June 30, 2015 to compare health care use and pregnancy complications for 9,124 women who used emergency shelter with those for 8,757 similar women who did not. Rates of mental illness and substance use disorders were significantly higher among homeless women. Adjusted odds of having nine pregnancy complications were also significantly higher for homeless women and remained substantially unchanged after we adjusted for behavioral health disorders. Emergency shelter users also had fewer ambulatory care visits and more months without billable care and were more likely to visit an emergency department. Homelessness and behavioral health disorders appear to be independent factors contributing to pregnancy complications and should be addressed simultaneously.