Alfalfa, Medicago sativa L., is an important forage crop in the U.S. and worldwide. However, in acid soil, its productivity and persistence dramatically decrease. Acid-soil syndrome causes a severe toxicity that inhibits root growth and development exacerbated by Al+3. Breeding and genomic approaches to improve acid/Al tolerance provide new opportunities to grow alfalfa in lands considered marginal for alfalfa growth. In this study, three different approaches were used to identify and to evaluate acid/Al tolerance in alfalfa: (1) identification and mapping of quantitative trait loci (QTL) associated with acid/Al tolerance, (2) evaluation of transgenic plants over-expressing Pseudomonas aeruginosa citrate synthase (CS) and/or a gene coding for a plasma membrane H+-ATPase from Daucus carota (DcPA1), and (3) comparison of genetic gain for acid/Al tolerance as assessed by seedling biomass production in acidic soil under greenhouse conditions. Single-factor analysis and interval mapping identified QTL for Al tolerance on Altet-4 and on NECS-141 linkage groups. The phenotypic variation explained by individual QTL ranged from 9.5 to 35.3%. Some of these QTL were detected in multiple environments and for multiple traits while others were environment-specific. Four isogenic T2 populations, containing neither, one, or both transgenes (CS+DcPA1) were evaluated for acid/Al tolerance. The transgenic populations containing either CS or DcPA1 or both genes showed higher acid/Al tolerance than the non-transgenic population. No advantage of combining both transgenes in the same genetic background was observed. Lower levels of Al in shoot tissue were observed for the transgenic populations over the non-transgenic population. The comparison of selection methods showed that the phenotypic recurrent selection with gridding in unlimed soil was most effective at improving the Bulldog 805 population for shoot dry weight. This method of selection was the most effective in terms of the resources used and the responses achieved. Direct selection in unlimed soil resulted in increased alfalfa growth in acid and Al-rich soils compared to selection in limed soil. The information generated in these three experiments can be useful in improving our understanding of acid/Al tolerance in alfalfa and in developing cost-effective and efficient methods to obtain enhanced alfalfa germplasm in the future.