Aluminum (Al) toxicity is the major limiting factor for plant productivity on acid soils. Although it is clear that certain plant genotypes have evolved mechanisms that confer Al tolerance, the cellular and molecular basis for Al tolerance is still poorly understood. The objectives of this dissertation were (1) the genetic and physical characterization of a major gene for Al tolerance in wheat (Triticum aestivum L.) and (2) the identification of novel Al-responsive genes in rye (Secale cereale L.) to understand additional molecular mechanisms involved in the response of plants to Al-stress. The long arm of chromosome 4D in wheat harbors a major dominant gene conferring Al tolerance (Alt2 in 'Chinese Spring' and Alt BH in 'BH 1146'). In this study, we developed a more extensive genetic linkage map of the chromosome arm 4DL based on RFLP, SSR and AFLP markers, delimiting the Alt BH gene to a 5.9 cM interval between markers Xgdm125 and Xpsr914 . In addition, utilizing a set of wheat deletion lines for chromosome arm 4DL, the Alt BH gene was physically mapped to the distal region of the chromosome, between deletion breakpoints 0.70 and 0.86. Finally, analysis of 1 Mb of contiguous sequence of Arabidopsis chromosome 5 flanking the gene homologous to the BCD 1230 clone (a cosegregating marker in our population) revealed a previously identified region of stress-related and disease-resistance genes. This could explain the low level of polymorphism detected in the chromosome arm 4DL in hexaploid wheat. In addition, an EST approach was used to analyze changes in gene expression in roots of rye cv Blanco under Al stress. Comparison of two data sets from non-stressed and stressed cDNA libraries (774 and 1194 ESTs, respectively) was performed. A total of 671 known-function genes were used to analyze gene expression profiles. Many of the previously identified Al-responsive genes showed differences between both libraries. Certain genes were selected and their expression patterns studied using Northern hybridization. A total of 13 novel genes involved in cell elongation and division, oxidative-stress, iron metabolism, and other cellular mechanisms were regulated by Al stress. These genes provide new insights about the response of Al-tolerant plants to toxic levels of Al.