The importance of alternative splicing in many genomes has raised interesting questions about its role in evolution. We previously reported that alternative splicing appears to be associated with an increased rate of recent exon creation / loss events, and proposed that it can reduce negative selection pressure on sequence regions that are alternatively spliced. In this paper we test this idea directly, using the occurrence of premature protein truncation events as a metric of selection pressure. We have analyzed 13,384 full-length transcript isoforms from human and 2,227 isoforms from mouse to identify sequences containing premature termination codons (PTC) that are likely targets of mRNA nonsense mediated decay. We found that alternatively spliced isoforms indeed had a much higher frequency of PTCs (11.1%) compared with the major transcript form of each gene (3.7%). However, this effect was strongly influenced by the chromosomal location of the gene: on the X chromosome, which is generally expressed as a single copy, the overall PTC rate was much lower (3.5%, vs. 8.9% on diploid autosomes), and the effect of alternative splicing was enhanced, causing a four-fold reduction in negative selection against PTC. Thus, diploidy and alternative splicing each increased tolerance for PTC by about three-fold, as approximately additive effects. These data may suggest genomic evidence that nonsense mediated decay has itself reduced negative selection pressure during evolution, via rapid degradation of aberrant transcripts that might yield dominant negative phenotypes.