In this paper we investigate rods made of nonlinearly elastic, composite-materials that feature a micro-heterogeneous prestrain that oscillates (locally periodic) on a scale that is small compared to the length of the rod. As a main result we derive a homogenized bending-torsion theory for rods as Gamma-limit from 3D nonlinear elasticity by simultaneous homogenization and dimension reduction under the assumption that the prestrain is of the order of the diameter of the rod. The limit model features a spontaneous curvature-torsion tensor that captures the macroscopic effect of the micro-heterogeneous prestrain. We devise a formula that allows to compute the spontaneous curvature-torsion tensor by means of a weighted average of the given prestrain. The weight in the average depends on the geometry of the composite and invokes correctors that are defined with help of boundary value problems for the system of linear elasticity. The definition of the correctors depends on a relative scaling parameter gamma, which monitors the ratio between the diameter of the rod and the period of the composite's microstructure. We observe an interesting size-effect: For the same prestrain a transition from flat minimizers to curved minimizers occurs by just changing the value of gamma. Moreover, in the paper we analytically investigate the microstructure-properties relation in the case of isotropic, layered composites, and consider applications to nematic liquid-crystal-elastomer rods and shape programming.