The Arabidopsis acaulis1-1 (acl1-1) mutant exhibits severe growth defects when grown at 22 degrees C. The leaves are tiny and curled and the inflorescence stems are short. We identified an inversion mutation in the original acl1-1 plants. The acl1-1 plants were crossed with Columbia wild-type, and the acl1-1 phenotype and the inversion were segregated in the F2 generation. Compared to the original acl1-1 plants with the inversion, the genuine acl1-1 plants without the inversion grew larger and their inflorescence stems grew longer at 22 degrees C. When the plants were grown at 24 degrees C, the differences in growth became more apparent. We investigated the expression of genes located in the inversion. Two genes that were located at each end of the inversion were disrupted, and full-length transcripts were not expressed. Expressions of some genes within and adjacent to the inversion were also altered. Our results indicate that the expression of multiple genes may be involved in the enhancement of the acl1-1 phenotype.