Cartilage collagens type II and type IX exist in two alternative forms which arise from alternative splicing and alternative use of promoters, respectively. In the present study we analyzed temporal and spatial expression patterns of the two isoforms of type II and type IX collagen transcripts as well as those of alpha2(IX) and alpha3(IX) collagen mRNAs in limb cartilages and eyes during mouse embryonic development. Northern and RNase protection assays revealed temporal coregulation of the two alternative isoforms in limbs, but not in the eye where no long form of alpha1(IX) collagen mRNA was detected. Although in situ hybridization of limbs revealed identical expression patterns of the long form of type II collagen and the short form of alpha1(IX) collagen mRNA in the perichondrium and periosteum of 14.5-18.5-day embryos, the patterns were distinctly different at day 12.5 of development: the long form of type II collagen mRNA was expressed throughout the developing cartilaginous anlage whereas the short form of alpha1(IX) collagen mRNA was expressed in the surrounding mesenchyme. Some differences were also detected in the temporal and spatial expression patterns between the alpha1(IX), alpha2(IX), and alpha3(IX) collagen mRNAs. In the eyes, alpha2(IX) collagen mRNA had highest expression levels at day 12.5, whereas alpha1(IX) and alpha3(IX) collagen mRNAs peaked later, at day 16.5. In the limbs, alpha1(IX) and alpha3(IX), but not alpha2(IX), collagen mRNAs were detected in periosteal cells after 16.5 days of development. In transgenic Dell mice, harboring type II collagen transgenes with a small deletion mutation, expression of mutant mRNA affected neither the alternative splicing of wild-type or mutant transcripts nor the ratio of the two alternative forms of the alpha1(IX) collagen mRNA. Despite some distinct similarities, the two alternative forms of type II and type IX collagen must, therefore, be under differential control during mouse development.