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Determining the higher level relationships of the modern amphibian order Gymnophiona (caecilians) poses a number of methodological problems. A cladistic methodology is outlined by which the phylogenetic relationships of this group can be determined objectively. Among the possible sister groups analyzed, which include dissorophid temnospondyls, aistopods, nectrideans, lysorophoids, microsaurs, anurans and urodeles, the microsaurs of the families Gymnarthridae and Goniorhynchidae are the most plausible sister group of caecilians, based on cranial osteology. Hence, the three modern orders of amphibians, caecilians, anurans and urodeles, do not constitute a monophyletic assemblage exclusive of all other groups. Ingroup analysis indicates that the Ichthyophiidae is the most primitive living caecilian family. The cladistic analysis suggests that features of the unique jaw apparatus define two groups of caecilians which diverged, phylogenetically, early in the group's history. Morphometric analysis reveals that elements of the jaw apparatus compose a functional suite of features. Aspects of the development, function, and significance of the jaw to miniaturization of the caecilian skull are inferred from the morphometric analysis.