The Hox genes are widely regarded as candidates for involvement in major evolutionary changes in body plan organization. We examine Hox gene expression data for several taxa, in relation to recent work on the polychaete annelid Chaetopterus. The work in Chaetopterus shows the basic conservation of colinearity of anterior expression boundaries seen in other groups. It also reveals novel patterns including early expression in the larval growth zone and later formation of posterior boundaries that correlate with morphological transitions in the polychaete body plan. The polychaete gene expression pattern is compared with those of Hox gene homologs in other taxa to reveal differences that represent evolutionary changes in Hox gene regulation between lineages. Correlations between Hox gene expression differences and morphological differences are examined, focussing on a number of cases in which posterior Hox gene expression boundaries correlate with morphological transitions. Differential regulation of these posterior expression boundaries is proposed as a possible mechanism for changes body plan regionalization.