A phylogenetic analysis of Jurassic irregular echinoids is realized to explore the origin and early evolution of this important subset of echinoids. The phylogeny is based on 39 characters and considers data from apical system architecture, the corona including tuberculation and spines, Aristotle’s lantern, and general test shape. Results corroborate the monophyly of Irregularia, and clarify the phylogenetic interrelationships existing between the main groups of irregular echinoids. Specializations of the Aristotle’s lantern, spines, tubercles and phyllodes constitute the apomorphies for different taxa, as for the whole of Irregularia. The phylogenetic signal yielded by these characters highlights the importance of the environmental context of the origin and diversification of irregular echinoids. The definition of ‘irregularity’ is re-examined, rejecting exocyclism and characters of the apical system as appropriate synapomorphies, and stressing the importance of other characters, particularly the high density and small size of tubercles and spines. A new clade name, Infraclypeidae [P], and phylocode designations (stem-based diagnoses) are proposed for the clades Irregularia, Eognathostomata, Microstomata, Neognathostomata and Atelostomata. Other groupings formerly used (Pygasteroida, Galeropygidae and Menopygidae) are considered paraphyletic.