Mutations in the sqt-1 and rol-6 cuticle collagen genes of Caenorhabditis elegans can cause dramatic alterations in organismal morphology. Genetic interactions and similarities in sequence and mutant phenotypes suggest that the sqt-1 and rol-6 collagen chains may physically interact. We show here that the sqt-1 and rol-6 genes are coordinately expressed during formation of the L2, L3, L4, adult, and L2d stage cuticles. Quantitative analyses indicate that the ratio of the steady-state levels of the sqt-1 and rol-6 mRNAs is approximately 2:1 at each of these stages, consistent with the possibility that they form a single heterotrimeric collagen. Surprisingly, the temporal expression patterns of sqt-1 and rol-6 mRNAs are not completely correlated with the times of appearance of their mutant phenotypes. Both sqt-1 and rol-6 mutant phenotypes appear in L2, L3, L4, adult, and L2d stage animals, and their mRNAs are easily detectable during synthesis of each of these cuticles. However, both sqt-1 and rol-6 mutant animals also display abnormal phenotypes at the dauer stage, but no transcripts from either gene are detected during synthesis of the dauer cuticle. We propose that dauer animals display a mutant phenotype in the absence of mutant collagen because they maintain the abnormal morphology that was generated in the preceding L2d stage.