Kearney, M. In press. Philosophy and Phylogenetics: Historical and Current Connections. Book chapter for "Cambridge Companion to the Philosophy of Biology". (David Hull and Michael Ruse, editors)

Rieppel, O., and M. Kearney. In press. The poverty of taxonomic characters. Biology and Philosophy.

Kley, N., and M. Kearney. In press. Adaptations to digging and burrowing. In press. Book chapter for "Fins and Limbs:  Evolution, Development and Transformation". (Brian K. Hall, editor)

Kearney, M., and O. Rieppel. 2006. Rejecting the 'Given' in systematics. Cladistics 22: 369-377.

Mahler, L., and M. Kearney. 2006. The palatal dentition in squamate reptiles. Fieldiana 1540:1-61.

Stuart, B. L., K. Dugan, M. W. Allard, and M. Kearney. 2006. Extraction of nuclear DNA from bone of skeletonized and fluid-preserved museum specimens. Systematics and Biodiversity 4:133-136.

Tsuihiji, T., M. Kearney, and O. Rieppel. 2006. First report of a pectoral girdle muscle in snakes, with comments on the snake cervico-dorsal boundary. Copeia 2006:206-215.

Maisano, J., M. Kearney, and T. Rowe. 2005. Cranial anatomy of the spade-headed amphisbaenian Diplometopon zarudnyi (Squamata, Amphisbaenia) based on high-resolution X-ray computed tomography. Journal of Morphology 267:70-102.

Rieppel, O., and M. Kearney. 2005. Tooth replacement in the Late Cretaceous mosasaur Clidastes. Journal of Herpetology 39:168-172. 

Kearney, M., J. Maisano, and T. Rowe. 2005. Cranial anatomy of the extinct worm lizard Rhineura hatcherii (Squamata, Amphisbaenia), based on High-Resolution X-Ray Computed Tomography. Journal of Morphology 264:1-33.

Kearney, M. and B.L. Stuart. 2004. Repeated evolution of limblessness and digging heads in worm lizards revealed by DNA from old bones. Proceedings of the Royal Society of London B 271:1677-1683.

Buckley, L., K. de Queiroz, and M. Kearney. 2004. Snake relationships and ambiguous data: a reply to Highton et al. Herpetological Review 35:117-121.

Kearney, M. 2003. Systematics and evolution of the Amphisbaenia: a phylogenetic hypothesis based on morphological evidence from fossil and recent forms. Herpetological Monographs 17:1-75.

Kearney, M. 2003. Diet in the amphisbaenian Bipes biporus. Journal of Herpetology 37:404-408.

Kearney, M. and J. M. Clark. 2003. Strategies for resolving ambiguity resulting from missing data in the phylogenetic analysis of extinct and living taxa: a critical review. Journal of Vertebrate Paleontology 23:263-274.

Kearney, M. 2003. The phylogenetic position of Sineoamphisbaena hexatabularis reexamined. Journal of Vertebrate Paleontology 23:394-403.

Kearney, M. 2002. Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions. Systematic Biology 51:369-381.

Rieppel, O. and M. Kearney. 2002. Similarity. Biological Journal of the Linnean Society 75(1):59-82.

Kearney, M. 2002. The appendicular skeleton in amphisbaenians. Copeia2002(3):719-738.

Rieppel, O. and M. Kearney. 2001. The origin of snakes: limits of a scientific debate. Biologist 2001(48):1-5.

Buckley, L., M. Kearney, and K. de Queiroz. 2000. Slowly-evolving protein loci and higher-level snake phylogeny: a reanalysis. Herpetologica 56:324-332.