We describe the spontaneous mutant mouse scoliosis <i>(sco)</i> that carries a new allele of <i>Pax1 (un-i, undulated intermediate)</i>. The <i>Pax1^un-i</i> allele is lacking the 5′-flanking region and exon 1 to 4 which is mapped to nt –2636 to –640 and –272 to 4271 of the <i>Pax1</i> gene. Homozygous mice show a mild form of the known phenotypes of other <i>Pax1</i> mutants. Adult mice have a lumbar scoliosis and kinky tails. In homozygous embryos the skeleton ossifies early, ossification centers of the vertebral bodies are fused with the ossification centers of the pedicles. Neural arches and spinous processes are underdeveloped but the pedicles and transverse processes are overdeveloped which is in contrast to other <i>Pax1</i> mutants. In the scapula, the acromion is missing and the deltoid tuberosity of the proximal humerus is shortened and thickened. Among the inner organs the thymus development is affected. In late embryos, the thymus is small and thymocyte numbers are reduced. T-cell development from CD4^– and CD8^– double negative (DN) to CD4⁺ and CD8⁺ double positive (DP) is decelerated. The percentage of CD90⁺ cells is also reduced but in contrast to other <i>Pax1</i> mutants no alteration of the expression level of the CD90 (Thy-1) could be found.