Somaclonal variation occurs among regenerants from tissue culture of many plant species. Our objective was to determine whether cytogenetic variation contributes to somaclonal variation in cotton (Gossyptum hirsutum L.,2n=4x=52). Of 117 somaclones of cotton regenerated from 18-month-old callus cultures of 'SJ-2' and 'SJ-5' cultivars, 35 were analyzed for meiotic abnormalities. The population of somaclones was extremely varied in phenotype, most plants being strikingly aberrant in phenotype. Fertility was generally poor: 84% failed to set bolls and only 5% set 10 or more bolls in a field environment. Only one of the somaclones (3%) formed 26 bivalents at metaphase I. Fourteen were nonsynaptic to partially synaptic at metaphase I. Synaptic abnormalities impaired fertility and precluded thorough metaphase analysis. Chromosome numbers obtained for 32 plants ranged from 49 to 53, and only 1 plant was hyperaneuploid. No plant was polyploid. Chromosomal abnormalities in plants with normal metaphase pairing included univalents, unequal bivalents, rod bivalents, trivalents, open quadrivalents, and centric fragments. Seventeen hypoaneuploid plants formed a V-shaped trivalent at metaphase I, constituting a high frequency of tertiary monosomy. The high frequencies of aneuploidy and tertiary monosomy indicate that cytogenetic anomalies are a major source of somaclonal variation in cotton. It is hypothesized that (i) primary cytogenetic events during cotton cell culture give rise to breakage fusion bridge (BFB) cycles, (ii) BFB cycles accrue during culture, (iii) BFB cycles cause loss of chromatin, and (iv) BFB cycles are resolved by the formation of stable tertiary chromosomes with mono-centric activity. The hypothesis accounts mechanistically for the coincidence of chromatin deficiencies and chromatin exchange involved implicitly in tertiary monosomy, as well as for the relatively high frequency of tertiary monosomy among somaclones.Key words: aneuploid, monosomic, synaptic, sterility, Gossypium.