Cotton (Gossypium hirsutum L.) yield and quality is affected by altered fruiting patterns with progress in season. The present study was conducted to analyse normal and altered (abnormal) boll (fruit) development at maturation phase. Both normal and abnormal bolls of the same age groups were analysed for growth in terms of dry weight, water content and endogenous abscisic acid (ABA) content of fibre and seed. Endogenous level of ABA was estimated by using antibodies raised against ABA–protein conjugate. To amplify the reaction, indirect ELISA (Enzyme Linked Immuno Sorbent Assay) was performed. A marked decrease in dry matter accumulation (DMA) of seed and fibre was observed in abnormal bolls as the season progressed. Fibre from the abnormal bolls showed marked variation in endogenous ABA content, however, in abnormal seeds water content and endogenous abscisic acid content showed significant variation compared to that of normal bolls. From the results, it is concluded that a marked decrease in seed dry weight may be because of a decrease in water content and accumulation of higher endogenous abscisic acid content, whereas, the major reason for reduced fibre weight may be due to accumulation of endogenous abscisic acid.