We recently completed genotyping the iCOGS chip, containing 206,000 selected single nucleotide polymorphisms (SNPs), in 180,993 breast and ovarian cancer cases and controls. We identified SNPs in 47 new loci that are associated with breast cancer risk (P<5x10-8) In addition to the loci already known, these loci explain 18% of the familial relative risk of breast cancer. The great majority of the SNPs are in or near genes not previously thought to be associated with breast cancer. An exception is TERT, which codes for the reverse transcriptase component of telomerase. To identify SNPs associated with telomere length (TL), breast or ovarian cancer risk, we analysed ~480 SNPs around TERT in 103,991 breast cancer cases and controls, 39,774 ovarian cancer cases and controls, and 11,705 BRCA1 mutation carriers, and measured TL in 53,724 controls. Associations with all phenotypes fall mainly into three independent peaks: in the TERT promoter (Peak 1), the minor alleles of SNPs correlated with rs2736108 associate with longer telomeres, reduced ER--breast cancer and reduced breast cancer risk in BRCA1 mutation carriers. In Peak 2, the minor allele of SNP rs7705526 associates with longer telomeres and increased low malignant potential ovarian cancer risk. In Peak 3, minor alleles of highly correlated SNPs, rs10069690 and rs2242652, are not associated with TL but increase risk of ER- -breast cancer, breast cancer in BRCA1 mutation carriers and serous invasive ovarian cancer, suggesting that these cancers share some common aetiology. We found that rs1006960 generates a novel, truncated TERT splice variant and showed with luciferase assays that some of the risk-associated SNPs are functional. Only the associations we found in Peak 1 support our original hypothesis that increased cancer risk is mediated through shorter telomeres. In summary, our data suggest that TERT has multiple roles in controlling TL and cancer development.