With increasing numbers of whole cancer genomes in the public domain, there is now significant interest in the identification of causal mutations that affect gene regulation. Recent pan-cancer analyses of mutations from hundreds of whole cancer genomes identified a surprisingly large number of recurrent mutations within the gene promoter regions^1,2. Nevertheless, with the exception of TERT^3,4, only promoter mutations of SDHD showed any significant correspondence with gene expression². The accumulation of promoter mutations is generally attributed to positive selection but why this occurs without corresponding alterations in gene expression lacks an adequate explanation. To address this we analysed 1500 cancer genomes across 17 cancer types overlapping mutations with DNase I hypersensitive (DHS) regions in proximal and distal gene regulatory elements. Melanomas, Lung and Ovarian cancers showed increased mutation density at core promoters (defined as +/-75 bp of a DHS within 1kb of transcription start sites), a phenomenon not present at distal enhancers. The increased promoter mutation rate in Melanoma was associated with an increase in overall sample mutation rate, without co-existing mutations in DNA repair genes. To understand the increased density of promoter mutations in these cancers, we compared the regulation and expression of genes with and without promoter mutations and found that mutated core promoters were associated with stronger transcriptional activity suggesting that transcriptional regulatory mechanisms at the core promoter may play a role in abrogating nucleotide excision repair. Finally, we compared the rates of rare and common single nucleotide polymorphisms (SNPs) at core promoters and noted that unlike other functional regions of the genome, the fraction of rare SNPs was significantly decreased, suggesting that core promoters are largely invariant to point mutations. Taken together our data demonstrate that frequent promoter mutations observed in cancer genomes may not be due to positive selection but result from a combination of neutral selection and increased transcriptional activity.