Depo-medroxyprogesterone acetate (DMPA) is an increasingly popular contraceptive choice among Navajo women. Weight gain is cited as a common side effect and major reason for discontinuation of DMPA. No controlled trials have evaluated the association between weight gain and DMPA in Navajo women. We aimed to clarify whether DMPA is associated with weight gain in Navajo women and to quantify the magnitude of weight gain. A cohort of 172 Navajo women who had used DMPA continuously for one or 2 years comprised the study group. A cohort of 134 Navajo women who used a non-progestin method or no method over 1 or 2 years comprised the comparison group. Initial weight, one-year weight and 2-year weights were recorded for all patients. Study subjects gained a mean of 6 pounds over one year and 11 pounds over 2 years relative to the comparison group (p < 0.001) after controlling for possible confounding variables including age, parity and initial weight. Use of DMPA is associated with significant weight gain in Navajo women. This weight gain is greater than that reported in previous uncontrolled studies in non-Navajo populations. This information should be utilized in counseling Navajo women about the side effects of DMPA.