Papillary carcinomas are a special histological type of breast cancer, and have a relatively good outcome. We characterised the genomic and phenotypic characteristics of papillary carcinomas, and to determine whether they would constitute an entity distinct from grade-and oestrogen receptor (ER)-matched invasive ductal carcinomas of no special type (IDC-NSTs). The phenotype of 63 papillary carcinomas of the breast and grade-and ER-matched IDC-NSTs was determined by immunohistochemistry. DNA of sufficient quality was extracted from 49 microdissected papillary carcinomas and 49 microdissected grade-and ER-matched IDC-NSTs. These samples were subjected to high-resolution microarray-based comparative genomic hybridisation (aCGH) and MassARRAY Sequenom sequencing analysis of 19 known oncogenes. Papillary carcinomas Conflict of Interest: NoneMicroarray comparative genomic hybridisation data, the analysis history, script and code are available at http://rock.icr.ac.uk/ collaborations/Mackay/Papillary.aCGH/. Europe PMC Funders GroupAuthor Manuscript J Pathol. Author manuscript; available in PMC 2016 July 27. Europe PMC Funders Author ManuscriptsEurope PMC Funders Author Manuscripts were predominantly of low histological grade, expressed immunohistochemical markers consistent with a luminal phenotype, and a lower rate of lymph node metastasis and p53 expression than grade-and ER-matched IDC-NSTs. Papillary carcinomas displayed less genomic aberrations than grade-and ER-matched IDC-NSTs; however the patterns of gene copy number aberrations found in papillary carcinomas were similar to those of ER-and grade-matched IDC-NSTs, including 16q losses. Furthermore, PIK3CA mutations were found in 43% and 29% of papillary carcinomas and grade-and ER-matched IDC-NSTs respectively. The genomic profiles of encapsulated, solid and invasive papillary carcinomas, the three morphological subtypes, were remarkably similar. Our results demonstrate that papillary carcinomas are a homogeneous special histological type of breast cancer. The similarities in the genomic profiles of papillary carcinomas and grade-and ERmatched IDC-NSTs suggest that papillary carcinomas may be best positioned as part of the spectrum of ER-positive breast cancers rather than as a distinct entity. Furthermore, the good prognosis of papillary carcinomas may stem from the low rates of lymph node metastasis and p53 expression, low number of gene copy number aberrations, and high prevalence of PIK3CA mutations.