Abstract The stability and free vibration analyses (i.e., buckling, natural frequencies and modal shapes) of an orthotropic singly symmetric 3D Timoshenko beam-column with generalized boundary conditions (i.e., with bending and torsional semirigid restraints and lateral bracings as well as lumped masses at both ends) subjected to an eccentric end axial load are presented in a classical manner. The five governing equations of dynamic equilibrium (i.e., two transverse shear equations, two bending moment equations and pure torsional moment equation) are sufficient to determine the natural frequencies and the corresponding modal shapes of the beam-column in the two principal planes of bending and torsion about its longitudinal axis. The proposed model includes the coupling effects among: (1) the deformations due to bending, shear and pure torsion; (2) inertias (translational, rotational and torsional) of all masses considered; (3) eccentric axial loads applied at the ends, and (4) restraints at the supports (bending, torsional and lateral bracings at both ends of the member). However, the effects of axial deformations and warping torsion produced by the axial load are not included; consequently the proposed model is not capable of capturing the phenomena of torsional buckling or combined lateral bending–torsional buckling. The proposed analytical model indicates that the stability and dynamic response of beam-columns are highly sensitive to the coupling effects, particularly in members with both ends free to rotate. The natural frequencies and modal shapes can be determined from the eigenvalues of a full 4×4 matrix for vibration in the plane of symmetry (using the uncoupled equations of transverse force and moment equilibrium at both ends) and from a full 6×6 matrix for the coupled shear–bending–torsional vibration (using the coupled equations of transverse shear, bending and torsional moment equilibrium at both ends). Also, it is shown that the proposed method reproduces the phenomena of modal interchanges (e.g. the second mode becoming the first mode and vise versa, etc.) when the bending and torsional restraints at the ends of the beam-column become very low. Four illustrative examples are presented showing the advantages and limitations of the proposed method.