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The determination of the historical relationships among snakes and between snakes and other squamates has remained problematical due to the combined problems of morphological character homoplasies and polarity misinterpretations coupled with the highly specialized body plan of the Serpentes. In order to provide an independent dataset and to escape the complex polarity and character choice problems inherent in a morphological investigation, 1,033 nucleotides of a mitochondrial DNA fragment encompassing both the ND4 protein-coding subunit and the His, Ser, and Leu tRNAs were sequenced and analyzed under parsimony criteria for a broad range of taxa from nearly all snake families using the outgroup method for correct character polarity. This investigation determined the origin of the snakes to be within the lizard clade and postulates an anguimorph lizard ancestry for the snakes. Subsequently, the relationships among the higher categories of snakes were evaluated and the results support both the conventional higher partitioning of the suborder Serpentes and a basal Scolecophidian clade, which had been previously supported by the morphological data. Examination of the Henophidia delineated two lineages, the Boidae and Pythonidae, which are monophyletic. The Pythonidae is expanded to include the Cylindrophinae, Loxoceminae, and Xenopeltinae and subsequent analyses provide support for an African and/or Asian origin of the Pythonidae. Historically problematical distributions for the boa genus Candoia and the python genus Loxocemus are paralleled in other lizard groups and do not represent a pattern from colonization events, but rather the relictual pattern derived from extinctions. The phylogenetic position of the enigmatic taxon Calabaria reinhardtii remains ambiguous from these data. This investigation, which represents one of the first systematic evaluations of snakes to utilize DNA sequence data, corroborates several features of the present morphologically deduced classifications. It simultaneously clarifies some of the long-standing problems of the relationships within Henophidia and also provides a new perspective on both the age of the groups of snakes in general and on the biogeographical events which shaped the modern distributions of these reptiles.