This paper introduces, analyzes and validates isogeometric mortar methods for the solution of thick shells problems which are set on a multipatch geometry. A particular attention will be devoted to the introduction of a proper formulation of the coupling conditions, with a particular interest on augmented lagrangian formulations, to the choice and validation of mortar spaces, and to the derivation of adequate integration rules. The relevance of the proposed approach is assessed numerically on various significative examples.