  We study dynamical baryons in the holographic QCD model of Sakai and Sugimoto
in the case of three flavors and with special interest in the construction of
the Chern-Simons (CS) term. The baryon classical solution in this model is
given by the BPST instanton, and we carry out the collective coordinate
quantization of the solution. The CS term should give rise to a first class
constraint which selects baryon states with right spins. However, the original
CS term written in terms of the CS 5-form does not work. We instead propose a
new CS term which is gauge invariant and is given as an integral over a six
dimensional space having as its boundary the original five dimensional
spacetime of the holographic model. Collective coordinate quantization using
our new CS term leads to correct baryon states and their mass formula.
