The advent of chromosome painting has brought the realization that structural aberrations can be far more complicated than previously imagined. Various investigators have devised their own nomenclature systems to deal with this difficulty, with the result that the terminology has become inconsistent and confusing. Recently, an international group of cytogeneticists experienced in chromosome painting gathered to address this issue. Results of the meeting are presented in this report, which provides a nomenclature system capable of describing chromosome aberrations that occur between painted and unpainted chromosomes, as well as aberrations involving only painted chromosomes. The nomenclature is flexible enough to describe accurately even the extensively rearranged chromosomes. As a consequence of this flexibility, the scheme upon which the nomenclature is based differs substantially from other systems of aberration classification. We call this system the Protocol for Aberration Identification and Nomenclature Terminology (PAINT).