The characterization of the conventional and organic cotton fibres to understand the differences present between them is presented. The cotton fibres were characterized for their fibre properties such as the surface morphology, surface chemical composition, surface elemental composition and internal fibre structure. The results show that the surface morphology and surface chemical composition of both the cotton fibres are similar. The surface elemental composition of both the cotton fibres shows that organic cotton fibres have higher percentage of metals than the conventional cotton fibres. Based on the FTIR spectrum analysis, it is observed that the organic cotton fibres may have a higher proportion of representative groups compared to that of the conventional cotton fibres. The fraction of I α and I β cellulose shows that I β cellulose dominates in both cotton fibres. The crystallinity of both the cotton fibres was determined using the wide angle X-ray diffraction data. The results show that crystallinity of both fibres is similar.