This book consists of research papers that cover the scientific areas of the International Workshop on Operator Theory, Operator Algebras and Applications, held in Lisbon in September 2012. The volume particularly focuses on (i) operator theory and harmonic analysis (singular integral operators with shifts; pseudodifferential operators, factorization of almost periodic matrix functions; inequalities; Cauchy type integrals; maximal and singular operators on generalized Orlicz-Morrey spaces; the Riesz potential operator; modification of Hadamard fractional integro-differentiation), (ii) operator algebras (invertibility in groupoid C-algebras; inner endomorphisms of some semi group, crossed products; C-algebras generated by mappings which have finite orbits; Folner sequences in operator algebras; arithmetic aspect of Cr SL(2); C-algebras of singular integral operators; algebras of operator sequences) and (iii) mathematical physics (operator approach to diffraction from polygonal-conical screens; Poisson geometry of difference Lax operators).