Worldwide, water stress during vegetative and reproductive development of cereal species is the most important constraint to crop yield. In maize (Zea mays L.), environmental stresses such as high temperature and drought affect yield by reducing the number and mean dry weight of harvested seeds per unit area. Total grain yield is of great economic concern, and preserving yield has received the most attention by public and private breeding programs. But environmental effects on grain quality is of equal concern as maize production becomes more focused on end-user traits specifically for utilization in markets such as dry-grind ethanol that are affected by the composition and quality of maize grain. This research tested the hypothesis that water stress during the later stages of grain filling influences starch structural properties through altered starch synthesis gene expression. Plants of the maize inbred B73 were grown under controlled water deficit conditions (leaf Ψ_w) of -1.2 MPa, -1.8 MPa, and terminal stress imposed at 14 days after pollination (DAP). Throughout the period of starch accumulation, 12 DAP – physiological maturity, kernels were harvested and analyzed by quantitative RT-PCR for expression of the major genes involved in the starch biosynthetic pathway: Shrunken2, Brittle2, Brittle1, Waxy, Sugary2, SBE1, and SBE2. Corresponding amylose and amylopectin content were measured as well as amylopectin branching characteristics. The results indicate that the starch biosynthetic genes are differentially affected by water stress during grain filling, which results in altered starch structure.