Balancing selection is one mechanism that may explain why diversity is maintained in wild populations. However, relatively few examples of genes showing evidence of balancing selection have been identified, particularly in plants. In this issue, Reininga et al. (2009) present three Arabidopsis loci that show strong evidence of balancing selection. The loci, discovered using a genome-scanning approach, encode proteins with diverse predicted functions: starch synthesis and control of gene expression. These three genes were identified by scanning only a small fraction of the Arabidopsis genome, suggesting that balancing selection may be more prevalent than previously known.