Summary: CGHnormaliter is a package for normalization of array comparative genomic hybridization (aCGH) data. It uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs). CGHnormaliter is integrated in the Bioconductor environment allowing a smooth link to visualization tools and further data analysis. Availability and Implementation: The CGHnormaliter package is implemented in R and under GPL 3.0 license available at Bioconductor: http://www.bioconductor.org. Contact: email@example.com. © The Author 2010. Published by Oxford University Press. All rights reserved. For Permissions, please email: firstname.lastname@example.org.