Subcortical volumes were quantitatively evaluated on clinical MRI exams of neurofibromatosis type 1 (NF1) and tuberous sclerosis complex (TSC) patients. Robustly larger volumes of several subcortical structures, including the thalamus, hippocampus and ventral diencephalon, were found in NF1; characteristic NF1 imaging abnormalities are found in these areas. In TSC, we found smaller cerebellar volumes; findings that have been associated with autistic phenotypes. Cluster analysis reveals three distinct clustering patterns, each corresponding to a patient class. These results show the feasibility of obtaining automatic quantitative measurements of anatomic structures from clinical MRI exams.