A Hopf algebroid is a possibly noncommutative generalization of a structure which is dual to a groupoid in the sense of space-algebra duality. In other words, function algebras on the space of objects and space of morphisms of a groupoid pack together in a structure of Hopf algebroid.
Given an internal groupoid in the category of affine algebraic -schemes, where is a field, the -algebras of global sections over the scheme of objects and scheme of morphisms have an additional structure of a commutative Hopf algebroid. In fact this is an antiequivalence of categories. Commutative Hopf algebroids are useful also in a version in brave new algebra? (the work of John Rognes).
There are several generalization to the noncommutative case. A difficult part is to work over the noncommutative base (i.e., the object of objects is noncommutative). The definition of a bialgebroid is not that difficult and there is even a very old definition due Takeuchi. To add an antipode is nontrivial. A definition of Lu from mid 1990s is rather nonselfdual unlike the case of Hopf algebras. So a better solution is to abandon the idea of an antipode and have some replacement for it. There are two approaches, one via monoidal bicategories due to Day and Street, and another due Gabi Böhm, using pairs of a left and right bialgebroid. Gabi has later shown that the two definitions are in fact equivalent.
The commutative version is classical, and there is an extensive literature. Some of the recent works on commutative case, related to homotopy theory and stacks are
The version in brave new algebra?
One can straightforwardly keep the base commutative while having the total algebra noncommutative, and the image of source and target maps are required to commute mutually. This version is due Maltsiniotis; he also generalized this to quasi-Hopf version:
Over a noncommutative base ring, there is a nonsymmetric version due J-H. Lu and a similar version is later studied by Ping Xu
The modern concept over the noncommutative base is discovered in two formally different formalisms, but the two concepts are equivalent:
B. Day, R. Street, Monoidal bicategories and Hopf algebroids, Advances in Mathematics 129, 1 (1997) 99–157
G. Böhm, An alternative notion of Hopf algebroid; in “Hopf algebras in noncommutative geometry and physics”, 31–53, Lecture Notes in Pure and Appl. Math. 239, Dekker, New York, 2005; math.QA/0301169
G. Böhm, Hopf algebroids, (a chapter of) Handbook of algebra, arxiv:math.RA/0805.3806