The Advanced Fiber Information System (AFIS) was used to evaluate cotton grown under conditions of significant drought stress. The effect of flowering date and branch position on fiber quality was evaluated using AFIS. AFIS quality parameters measured included fiber maturity, cell wall area, length (by weight and number), and short fiber content. Results of a statistically controlled experiment indicated that all properties vary significantly with flowering date, but, with the exception of short fiber content, there is no effect of boll position on a given branch.