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This work presents a quantitative measure, α, of the degree of segregation of two cell types in sections of aggregates, and some results obtained with the measure relating to ‘sorting out’. The method is designed particularly for the case where labelling of one type of cell is incomplete, and the importance of this effect is assessed. Possible problems in formulating such a model are discussed. The measure α is compared with methods used in investigations of segregation in plant communities. Segregation of chick heart and limb-bud cells in mixed aggregates has been analysed using α. In control aggregates of mixtures of labelled and unlabelled cells of one type, α is near to its random value of 1, and we suggest that the departure from random can be adequately accounted for by cell division. In mixed aggregates, significant segregation is consistently found, even in aggregates formed after 2 and 4 h. Both disaggregation procedures (EDTA, trypsin or trypsin+ EDTA) and reaggregation methods (reciprocating or gyratory shaker) are found to have an effect on the degree of segregation. Possible reasons for these findings are discussed. Positioning of the cells relative to the outside of aggregates is also investigated for some of the aggregates.