SNP-LOH was successful in 31/35 samples. LOH events were more common in classical LCIS with associated ILC compared with pure LCIS. Commonest changes were on 16q and 1q. Other areas of LOH were more common in LCIS associated with ILC but did not reach statistical significance. Patterns of genetic change were maintained in ILC compared with the associated LCIS and 3/5 cases acquired additional genetic changes. Copy number changes were confirmed in three cases using BAC arrays. Concordance for copy number gain and loss was 50% and 75%, respectively. Concordance for copy neutral LOH was 100%. Ploidy studies on 20 cases revealed that all cases of classical LCIS were diploid whereas 5/9 pleomorphic LCIS/ILC samples were tetraploid or aneuploid.