Some evidence suggests that phytoestrogens, such as soy-derived isoflavones, may have beneficial effects on cardiovascular health and glycemic control. These data are mainly limited to postmenopausal women or individuals at elevated cardiometabolic risk. There is a lack of data for pregnant women who have elevated estrogen levels and physiologically altered glucose and lipid metabolism. We analyzed data from 299 pregnant women who participated in the NHANES 2001-2008 surveys. Multivariable linear regression analyses were used to examine the association between urinary concentrations of isoflavonoids and cardiometabolic risk markers, adjusted for body mass index, pregnancy trimester, total energy intake, dietary intake of protein, fiber, and cholesterol, and demographic and lifestyle factors. Cardiometabolic risk markers were log-transformed, and geometric means were calculated by quartiles of urinary concentrations of isoflavonoids. Comparing women in the highest vs. lowest quartiles of urine total isoflavone concentrations, we observed significant, inverse associations with circulating concentrations of fasting glucose (79 vs. 88 mg/dL, P-trend = 0.0009), insulin (8.2 vs. 12.8 muU/mL, P-trend = 0.03), and triglyceride (156 vs. 185 mg/dL, P-trend = 0.02), and the homeostasis model assessment of insulin resistance (1.6 vs. 2.8, P-trend = 0.01), but not for total, low-density lipoprotein cholesterol and high-density lipoprotein cholesterol. The concentrations of individual isoflavonoids, daidzein, equol, and O-desmethylangolensin were inversely associated with some cardiometabolic risk markers, although no clear pattern emerged. These data suggest that there may be a relation between isoflavone intake and cardiometabolic risk markers in pregnant women.