Our aim was to evaluate the relationship between the neurological outcome of tuberous sclerosis complex (TSC) and the findings obtained from both cranial magnetic resonance imaging (MRI) and single voxel proton spectroscopy (SVPS). MRIs of 13 children who met the diagnostic criteria for TSC were taken. Eleven of these children also underwent a prospective analysis of SVPS. Fisher's exact test and Mann-Whitney U test were used, where applicable, to detect any signs of the imaging data that would indicate poor outcome, or in other words, poor seizure control and/ or high degree of mental retardation. Poor seizure control was seen in eight of the patients and multiple seizure types in seven. Mental retardation was severe in six patients and mild/moderate in seven. MRI revealed multiple bilateral tubers and subependymal nodules (13/13), confluence of tubers (8/13), subcortical linear heterotopias (7/13), gyral cores (3/13) and cortical atrophy (3/13). SVPS findings of tubers were characterized by decreased NAA/Cr (1.43 +/- 0.33, p<0.001), increased Cho/Cr (0.91 +/- 0.082, p< 0.05) and mI/Cr (0.97 +/- 0.19, p<0.01) ratios when compared with those of the control group. Lactate peak was detected in six patients. Unfavorable outcome in TSC can be predicted with the help of the following: multiple seizure types, a number of confluent appearances of the tubers and cortical atrophy. SVPS could be a useful clue to understand the pathophysiologic function of the tubers, especially in children with refractory epilepsy along with TSC.