Meiotic recombination can be affected by factors that reside either within (i.e., cis-acting elements) or outside (i.e., trans -acting modifiers) the recombining interval. To assess how trans-acting genetic modifiers polymorphic within maize germplasm affect rates and patterns of meiotic recombination in the absence of polymorphic cis factors, meiotic recombination was characterized across a sequence-identical 140-kb multi-genic a1-sh2 interval in each of three genetic backgrounds in maize. Rates of recombination among the genetic backgrounds varied twofold. The distributions of recombination breakpoints across the a1-sh2 interval in each background established that trans -acting modifier(s) polymorphic among genetic backgrounds can increase or decrease rates of recombination in both genic and intergenic regions over relatively small genetic and physical intervals and can even convert a region to a recombination hotspot. In addition, at least some trans-acting modifiers do not globally affect recombination, but instead target specific regions of the genome. To study a potential trans-acting modifier, recombination at an a1 allele containing a non-autonomous Mu1 insertion was assayed in both the presence and absence of the corresponding autonomous transposon, MuDR. In the presence of MuDR the rate of crossing over increased by fourfold, thereby demonstrating that MuDR is a trans-acting modifier of meiotic recombination. Because MuDR catalyzes the excision of Mu1, this is the first in vivo evidence that DNA breaks stimulate meiotic recombination in plants. In addition to trans-acting modifiers, the effects of A1-b, a tandem gene duplication of the maize a1 locus and a cis-acting factor, on meiotic recombination were characterized. This study directly demonstrates that in this genotype the homolog is the preferred template for unequal recombination and that interchromatid recombination is regulated separately from interhomolog recombination (e.g., recombination breakpoints resolve differently between the two recombination templates). Regulation of unequal recombination appears to occur at many levels including the chromosome (i.e., sister chromatid vs. homolog recombination) and the components of the duplication (i.e., pairing configurations). Rates of unequal recombination at A1-b are similar to the rate of recombination between non-duplicated a1 alleles. Unequal recombination is therefore common and is likely to be responsible for the generation of genetic variability, even within inbred lines.