Background: Unstable carotid plaques that consist of large lipid pool and intraplaque hemorrhage are more likely to cause cerebral infarction. We previously developed an integrated backscatter (IBS) ultrasound color-coded mapping method to evaluate the tissue characteristics of plaques. The purpose of this study was to determine whether 3-dimensional IBS color-coded mapping and signal intensity ratio (SIR) from magnetic resonance imaging (MRI) could distinguish the early symptomatic plaques from late symptomatic plaques. Methods: We performed quantitative tissue characterization of carotid plaques measuring IBS values and the SIR from T1-weighted MRI images in 95 carotid plaques (>50% stenosis) in 95 patients (45 symptomatic, 50 asymptomatic). Results: The percent unstable component volume (UCV) that consisted of lipid pool and intraplaque hemorrhage and the SIR of symptomatic carotid plaques were higher than those of asymptomatic plaques (57.8 ± 25.1 vs. 46.8 ± 25.1%, p = 0.036; 1.31 ± 0.25 vs. 1.21 ± 0.26, p = 0.047). In patients that were imaged within 3 days of symptom onset, the %UCV and SIR were significantly higher than the values in patients that were imaged 30–180 days after symptom onset (73.1 ± 18.4 vs. 38.7 ± 18.4%, p < 0.001; 1.38 ± 0.22 vs. 1.22 ± 0.26, p = 0.031). From the analysis of receiver operating characteristic curves, a %UCV of 50% (measured by IBS) and an SIR of 1.25 (measured by MRI) were the most optimal cutoff values for identifying early symptomatic plaques. Conclusions: Noninvasive quantitative tissue characterization of atherosclerotic lesions in carotid arteries using IBS ultrasound and MRI is useful to distinguish early symptomatic plaques from late symptomatic plaques.