The objectives of this study were (1) to test the utility of tuber count and tuber location as biomarkers of disease severity in patients with tuberous sclerosis complex and (2) to examine the relationship between gene mutation, tuber count, and tuber location. We found that an increased tuber count per lobe and in total was associated with an increased risk of infantile spasms (P < .01). Increased tuber count in the occipital lobe was associated with an increased risk of pervasive developmental disorder (P = .0074). The mean tuber count per lobe and in total was higher in those with poorly controlled seizures and those with off-track development; however, these differences were not statistically significant (P > .01). The TSC2 gene mutation was associated with a significant increase in the tuber count per lobe and in total (P < .01). In summary, increased tuber count is strongly associated with infantile spasms and a TSC2 gene mutation. Seizure control and developmental delay do not show the strong association with tuber count suggested by the earlier literature.