In May 1971, Illusie defended a state doctorate entitled "Cotangent complex; application to the theory of deformations" at the University of Paris-Sud, in front of a jury composed of Alexander Grothendieck, Michel Demazure and Jean-Pierre Serre and presided by Henri Cartan. The thesis was published in French by Springer-Verlag as a two-volume book. The main results of the thesis are summarized in a paper in English presented in Halifax, at Dalhousie University, on January 1971 as part of a colloquium on algebraic geometry. This paper, originally published by Springer-Verlag in 1972, also exists in a slightly extended version. Illusie's construction of the cotangent complex generalizes that of Michel André and Daniel Quillen to morphisms of ringed topoi. The generality of the framework makes it possible to apply the formalism to various first-order deformation problems: schemes, morphisms of schemes, group schemes and torsors under group schemes. Results concerning commutative group schemes in particular were the key tool in Grothendieck's proof of his existence and structure theorem for infinitesimal deformations of Barsotti–Tate groups, an ingredient in Gerd Faltings' proof of the Mordell conjecture. In Chapter VIII of the second volume of the thesis, Illusie introduces and studies derived de Rham complexes.
Cohomologie ℓ-adique et fonctions L, Séminaire de Géométrie Algébrique du Bois-Marie 1965-66, SGA 5, dir. A. Grothendieck, Lecture Notes in Mathematics 589, Berlin and New York, Springer, 1977.
, Théorie des intersections et théorème de Riemann–Roch, Séminaire de Géométrie Algébrique du Bois Marie 1966–67, SGA 6, Lecture Notes in Mathematics 225, Berlin and New York, Springer, 1971.
"Complexe de de Rham–Witt et cohomologie cristalline", Annales Scientifiques de l'École Normale Supérieure, 1979, ser. 4, vol. 12, 4, pp. 501–661, url=http://archive.numdam.org/ARCHIVE/ASENS/ASENS_1979_4_12_4/ASENS_1979_4_12_4_501_0/ASENS_1979_4_12_4_501_0.pdf.
, Surfaces algébriques, Séminaire de géométrie algébrique d'Orsay 1976–78, Lecture Notes in Mathematics 868, Berlin and New York, Springer, 1981.
, "Les suites spectrales ssociées au complexe de De Rham–Witt", Publ. Math. IHES, vol. 57, 1983, pp. 73–212.
,"Relèvements modulo p2 et décomposition du complexe de de Rham", Inv. math., vol. 89, pp. 247–270.
"Sur la formule de Picard–Lefschetz", in Algebraic Geometry 2000, ed. Azumino, Advanced Studies in Pure Mathematics 36, 2002, pp. 249–268, Mathematical Society of Japan,Tokyo.