The effects of cotton plant structure on cotton lint yield and fiber quality were determined for a short-season cultivar, TAMCOT CD3H. An existing cotton plant model, COTSIM, was adapted to short-season cultivation by using growth parameters estimated for TAMCOT CD3H. The cotton plant model was further modified to include plant fruiting structure. Quality parameters and yield of individual fruits at different nodal positions were determined for the test cultivar. Those fruiting positions that contributed similarly to yield and quality were grouped into corresponding 'quality' arrays. The development of fruit cohorts was modeled using an algorithm that simulates the distribution of growth rates with a time distributed delay. This algorithm was extended to include quality arrays. The inclusion of the effects of plant structure on cotton yield and quality permits a more rational calculation of expected price. Additionally, when linked to insect pest models, this model will simulate a dynamic, position-dependent effect of insect damage on fruiting structures and ultimate economic loss.