In this paper a boundary element method is developed for the general flexural-torsional buckling analysis of Timoshenko beams of arbitrarily shaped cross section. The beam is subjected to a compressive centrally applied concentrated axial load together with arbitrarily axial, transverse and torsional distributed loading, while its edges are restrained by the most general linear boundary conditions. The resulting boundary value problem, described by three coupled ordinary differential equations, is solved employing a boundary integral equation approach. All basic equations are formulated with respect to the principal shear axes coordinate system, which does not coincide with the principal bending one in a nonsymmetric cross section. To account for shear deformations, the concept of shear deformation coefficients is used. Six coupled boundary value problems are formulated with respect to the transverse displacements, to the angle of twist, to the primary warping function and to two stress functions and solved using the Analog Equation Method, a BEM based method. Several beams are analysed to illustrate the method and demonstrate its efficiency and wherever possible its accuracy. The range of applicability of the thin-walled theory and the significant influence of the boundary conditions and the shear deformation effect on the buckling load are investigated through examples with great practical interest.