The MR appearance of clots with different internal structures was compared on gradient-echo (GE) and spin-echo (SE) images. After MR imaging, clots were submitted for histological analysis to allow direct correlation of clot structure with MR image intensity. Normal heterogeneous clots (containing entrapped serum) were hypointense compared to both unclotted blood (Hct 45) and brain on GE MR images. Homogeneous (serum-poor) clots and settled blood were hyperintense to unclotted blood and isointense or hyperintense to brain. These results indicate that the GE technique is quite sensitive to the physical inhomogeneity created (at the voxel level) when blood forms an inhomogeneous clot containing relatively large islands of red blood cells (RBCs) surrounded by lakes of serum. The effect of the different possible clot structures on GE signal intensity thus provides an etiology for the previously unexplained observations of hemorrhage with high signal intensity on GE MR images.