The taxonomy of the shrews (family Soricidae) is primarily underpinned by the analysis of morphology characters. These morphological characters are, however, often plesiomorphic and difficult to interpret in an evolutionarily meaningful way. Recent molecular studies have provided some clarity at lower-taxonomic levels, but studies giving resolution to deeper levels of the soricid phylogeny are lacking. By constructing the most taxonomically inclusive molecular phylogeny for this cosmopolitan family, this study aims to test the utility of the routinely used mitochondrial cytochrome b gene to resolve the higher-level relationships within the Soricidae. Given the life history characteristics of shrews (high metabolic rate in Soricinae, small body size, fast generation time and generally short life span), the metabolic theory predicts accelerated nucleotide turnover in this family. By examining the molecular evolution of the cytochrome b molecule, this study identifies both lineage- and codon-specific mutational rate differences. We suggest that codon-specific mutational rate patterns are best explained by unique selective regimes operating on the different codon positions, while lineage-specific rate variation among genera belonging to Soricidae may reflect differences in the mode and speed of speciation events which generated species.