We study the structure of symmetric vortices in a Ginzburg–Landau model based on Zhang's SO(5) theory of high-temperature superconductivity and antiferromagnetism. We consider both a full Ginzburg–Landau theory (with Ginzburg–Landau scaling parameter κ < ∞) and a κ → ∞ limiting model. In all cases we find that the usual superconducting vortices (with normal phase in the central core region) become unstable (not energy minimizing) when the chemical potential crosses a threshold level, giving rise to a new vortex profile with antiferromagnetic ordering in the core region. We show that this phase transition in the cores is due to a bifurcation from a simple eigenvalue of the linearized equations. In the limiting large-κ model, we prove that the antiferromagnetic core solutions are always non-degenerate local energy minimizers and prove an exact multiplicity result for physically relevant solutions.