Plant height in sorghum is a complex trait with at least 4 major loci, of which only Dw3 has been characterized. Dw3 encodes a phosphoglycoprotein auxin efflux carrier orthologous to PGP1 in Arabidopsis. The recessive dw3 allele contains a tandem duplication and reverts back to a wild-type allele at low frequency due to unequal crossing-over; stable recessives at the Dw3 locus have also been reported. We used association mapping to investigate the effects of nucleotide variation at the Dw3 locus on plant and inflorescence architecture in a panel of 378 sorghum lines. Recessive dw3 plants have shortened lower vegetative internodes but longer apical structures, including both the inflorescence and the final vegetative internode. Drastically reduced variance in plant height across all recessive dw3 lines suggests that Dw3 is epistatic to other major height loci in sorghum, and expression analysis in near-isogenic lines shows that dw3 lines have altered gibberellin metabolism. Association mapping identifies a second gene, a GA2-oxidase involved in gibberellin inactivation, that associates very strongly with plant height. Dw3 and the GA2-oxidase interact with each other such that the effects of the GA2-oxidase are much stronger in a wild-type Dw3 background. In addition, we have found at least two novel, recessive alleles of dw3 that are expected to be stable. Dw3 was a target of the Sorghum Conversion Program, which converted tall, photoperiod-sensitive accessions to short, photoperiod-insensitive lines suitable for US grain production. As expected, the genomic region around Dw3 shows extensive linkage disequilibrium in Sorghum Conversion (SC) lines carrying the recessive allele, but not in SC lines carrying wild-type Dw3. We discuss prospects for the isolation of additional sorghum height and flowering time loci through a genome-wide scan.