Thermogravimetric analysis and Fourier Transform Infrared were used to study cotton fiber. Thermal analysis of cotton fiber showed the presence of three regions of thermal decomposition between 37ºC and 150ºC for region I, between 225ºC and 425ºC for region II, and between 425ºC and 600ºC for region III. Complete decomposition of the fiber occurred at 600ºC. The results showed significant effects of the fineness/maturity indicators on the weight loss and the peak temperatures in regions II and III. High micronaires (coarse or very mature fibers), high maturity ratios, and low standard fineness values are associated with low weight losses. However, high weight losses are associated with high primary cell wall areas per unit mass. The application of Fourier Transform Infrared microspectroscopy to study the structural properties of cotton fibers showed the importance of this technique in providing additional structural information not currently available through the standard testing techniques (HVI, AFIS).