1986

• Cavalier-Smith, T. 1986. The kingdom Chromista: origin and systematics. In: Progress in phycological research 4. (Round, F.E. & Chapman, D.J. Eds), pp. 309–347. Bristol: Bipress Ltd. Reference page. 

1987

• Cavalier-Smith T., 1987. The origin of eukaryote and archaebacterial cells, Ann NY Acad Sci, 503:17–54.

1993

• Cavalier-Smith T., 1993. Kingdom protozoa and its 18 phyla. Microbiology and Molecular Biology Reviews, Am Soc Microbiol., 1993 Dec;57(4):953-94, PMID: 8302218.
• Allsopp B.A., Baylis H.A., Allsopp M., Cavalier-Smith T.…, 1993. Discrimination between six species of Theileria using oligonucleotide probes which detect small subunit ribosomal RNA sequences. Parasitology.

• Cavalier-Smith, T. 1993. The origin, losses and gains of chloroplasts. In: Origins of plastids: symbiogenesis, prochlorophytes, and the origins of chloroplasts. (Lewin, R.A. Eds), pp. 291–349. New York: Chapman and Hall. DOI: 10.1007/978-1-4615-2818-0_15 . Reference page. 

1997

• Cavalier-Smith T., 1997. Cell and genome coevolution: facultative anaerobiosis, glycosomes and kinetoplastan RNA editing. Trends in Genetics.
• Cavalier-Smith T., 1997. Sagenista and Bigyra, two phyla of heterotrophic heterokont chromists. Archiv für Protistenkunde, Elsevier.
• Cavalier-Smith T., 1997. Amoeboflagellates and mitochondrial cristae in eukaryote evolution: megasystematics of the new protozoan subkingdoms Eozoa and Neozoa. Archiv für Protistenkunde, Elsevier.
• Cavalier-Smith T., Chad E.E., 1997. Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Archiv für Protistenkunde, Elsevier.
• …, PR Gilson, SE Douglas, T Cavalier-Smith, …, 1997. Bonsai genomics: sequencing the smallest eukaryotic genomes. Trends in Genetics.

1998

• Cavalier-Smith, T. 1998. A revised six-kingdom system of life. Biological Reviews of the Cambridge Philosophical Society 73: 203–266. Reference page. 

1999

• Cavalier-Smith T., 1999. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. Journal of Eukaryotic Microbiology 46(4), 347–366, DOI: 10.1111/j.1550-7408.1999.tb04614.x/full .
• …, Green B.R., Cavalier-Smith T., 1999. Diversification of a chimaeric algal group, the chlorarachniophytes: phylogeny of nuclear and nucleomorph small-subunit rRNA genes. Molecular Biology and …

2002

• Cavalier-Smith T., 2002. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol. 2002 Mar;52 (Pt 2) :297-354, DOI: 10.1099/00207713-52-2-297 .

• Cavalier-Smith, T. 2002. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionary Microbiology 52(Pt 1):7-76. DOI: 10.1099/00207713-52-1-7 . Reference page. 

2003

• Cavalier-Smith T., 2003. Protist phylogeny and the high-level classification of Protozoa. European Journal of Protistology 39: 338–348, DOI: 10.1078/0932-4739-00002 .
• Cavalier-Smith T., Chao E.E., 2003. Phylogeny and classification of phylum Cercozoa (Protozoa). Protist. 2003 Oct;154(3-4):341-58, PMID: 14658494, DOI: 10.1078/143446103322454112 .

2006

• Cavalier-Smith T., 2006. Rooting the tree of life by transition analyses. Biol. Direct, 1: 19. DOI: 10.1186/1745-6150-1-19

2008

• …, Orr R., Ruden T., Jakobsen K.S., Cavalier-Smith T., 2008. Multigene phylogeny of choanozoa and the origin of animals. PloS one.

2009

• Cavalier-Smith T., 2009. Megaphylogeny, Cell Body Plans, Adaptive Zones: Causes and Timing of Eukaryote Basal Radiations. Eukaryotic Microbiology, Volume 56, Issue 1, January/February 2009, Pages 26-33, DOI: 10.1111/j.1550-7408.2008.00373.x .

2012

• Cavalier-Smith, T. & Karpov, S.A. 2012. Paracercomonas kinetid ultrastructure, origins of the body plan of Cercomonadida, and cytoskeleton evolution in Cercozoa. Protist 163(1): 47–75. Abstract. DOI: 10.1016/j.protis.2011.06.004 Reference page. 

2015

• Ruggiero, M.A., Gordon, D.P., Orrell, T.M., Bailly, N., Bourgoin, T., Brusca, R.C., Cavalier-Smith, T., Guiry, M.D. & Kirk, P.M. 2015. A Higher Level Classification of All Living Organisms. PLoS ONE 10(4): e0119248 DOI: 10.1371/journal.pone.0119248 . [Correction in 10(6): e0130114 DOI: 10.1371/journal.pone.0130114 .] Reference page.