The L5178Y/TK+/- leads to TK-/- mouse lymphoma mutagen assay, which allows selection of forward mutations at the autosomal thymidine kinase (TK) locus, uses a TK+/- heterozygous cell line, TK+/- 3.7.2C. Quantitation of colonies of mutant TK-/- cells in the assay forms the basis for calculations of mutagenic potential of test compounds. We have evaluated the banded karyotypes of the parent TK+/- heterozygous cell line, as well as homozygous TK-/- mutants, in order to relate the genetic and morphological properties of mutant colonies. The parent cell line displays karyotype homogeneity, all cells containing normal mouse chromosomes, readily identifiable chromosome rearrangements, and cell line specific marker chromosomes. Mutant TK-/- colonies of the TK+/- 3.7.2C cell line form a bimodal frequency distribution of colony sizes for most mutagenic or carcinogenic test substances. Large-colony (lambda) TK-/- mutants with normal growth kinetics appear karyotypically identical within and among clones and with the TK+/- parental cell line. In contrast, most slow-growing small-colony (sigma) TK-/- mutants have readily recognizable chromosome rearrangements involving chromosome 11, which contains the thymidine kinase gene locus. It is possible that the heritable differences in growth kinetics and resultant colony morphology in lambda and sigma mutants are related to the type of chromosomal damage sustained. Large-colony mutants receive minimal damage, possibly in the form of point mutations at the TK locus, while small-colony mutants receive damage to other genetic functions coordinately with loss of TK activity, implying gross insult to chromosomal material. It seems likely that lambda and sigma mutants result from 2 different mutational mechanisms that may be distinguished on the basis of mutant colony morphology.