Tuberous sclerosis complex (TSC) is an autosomal dominant disorder that affects several organs in the human body including the brain, heart, kidneys, eyes, skin, spleen, liver and lungs [Roach, et al., 1999]. TSC is characterized by hamartomas that rarely progress to malignancy in the affected organs. Clinical symptoms of TSC include cortical tubers and subependymal nodules in the brain, seizures, mental retardation, ungual and periungual fibromas, angiofibromas of the face, and angiomyolipomas in the kidneys [Roach, et al., 1999]. TSC displays genetic heterogeneity with two known loci: TSC1 on chromosome 9q34 [Fryer, et al., 1987a] and TSC2 on chromosome 16p13.3 [Kandt, et al., 1992]. The genes for both loci have been isolated and characterized [ The European Chromosome 16 Tuberous Sclerosis Consortium, 1993; van Slegtenhorst, et al., 1997]. The TSC1 gene contains 21 coding and two non-coding exons and encodes for an 8.6 kb mRNA. It spans 45 kb of genomic DNA and codes for hamartin, a 1,164 amino acid protein of 130 kDa. The TSC2 encodes for a 200 kDa protein, tuberin, and spans 43 kb of genomic DNA. The TSC2 gene consists of 41 coding exons and one non-coding exon and encodes for a 5.4 kb mRNA. Both genes are known to function as tumor suppressors [Carbonara, et al., 1994; Green, et al., 1994a; Green, et al., 1994b]. Several groups have performed mutation analysis of both the genes in patients mainly from the western and Japanese populations. A total of 133 mutations in the TSC1 gene and 350 mutations in the TSC2 gene have been reported so far (Human Gene Mutation Database; http://archive.uwcm.ac.uk/uwcm/mg/hgmd0.html). However, there is no report on the mutation analysis of the TSC genes from the Indian population. In this study, a total of 24 TSC cases were ascertained from the Indian population and a comprehensive mutation analysis of both the TSC genes was carried out in them to understand the function of both the genes, to locate important domains and also to find the mutational hotspots for molecular diagnosis of TSC. A total of 12 mutations, including seven novel mutations were identified. It was also shown that the most recurrent mutations (c.1831C>T and c.1832G>A) are, in part, due to methylation of the CpG dinucleotide. There are still 15-25% TSC cases in western populations with undetected mutations [Cheadle, et al., 2000a]. Further, there are familial TSC cases linked either to the TSC1 on 9q34 or TSC2 on 16p13.3 which fail to show any mutations in the coding sequences of both genes [Cheadle, et al., 2000a]. The failure to detect mutations in these cases could be due to several reasons. First, it could be that the mutations lie in the regulatory regions (promoters and enhancers) of both the genes, presently unidentified for the TSC1 gene [Cheadle, et al., 2000a]. Second, it is possible that the mutations lie outside of the coding sequences, within intronic sequences, or in the 5’ or 3’ UTRs [Cheadle, et al., 2000a]. Third, it may be due to the limitation of the techniques used to identify mutations [Cheadle, et al., 2000a]. In order to look for mutations in the promoter, the TSC1 gene promoter was characterized using luciferase reporter gene transfection assay. The promoter for the TSC2 gene is known [Kobayashi, et al., 1997]. The promoters of both TSC1 and TSC2 genes were sequenced in all the 24 cases to look for mutations. During the characterization of the TSC1 gene promoter, a novel isoform involving the non-coding exon 1 of the TSC1 gene was discovered serendipitously.