Human and mouse genomes share similar long-range sequence organization, and have most of their genes being homologous. As alternative splicing is a frequent and important aspect of gene regulation, it is of interest to assess the level of conservation of alternative splicing. We examined mouse transcript data sets (EST and mRNA) for the presence of transcripts that both make spliced-alignment with the draft mouse genome sequence and demonstrate conservation of human transcript-confirmed alternative and constitutive splice junctions. This revealed 15% of alternative and 67% of constitutive splice junctions as conserved; however, these numbers are patently dependent on the extent of transcript coverage. Transcript coverage of conserved splice patterns is found to correlate well between human and mouse. A model, which extrapolates from observed levels of conservation at increasing levels of transcript support, estimates overall conservation of 61% of alternative and 74% of constitutive splice junctions, albeit with broad confidence intervals. Observed numbers of conserved alternative splicing events agreed with those expected on the basis of the model. Thus, it is apparent that many, and probably most, alternative splicing events are conserved between human and mouse. This, combined with the preservation of alternative frame stop codons in conserved frame breaking events, indicates a high level of commonality in patterns of gene expression between these two species. ; T. A. Thanaraj, Francis Clark and Juha Muilu