Second harmonic generation (SHG) results from molecules which are polarized by an external electric field often provided by an intense laser beam. The polarizability depends on firstly the intrinsic structural properties of the substance and hence the second-order nonlinear susceptibility, and secondly the intensity and polarization direction of the incident light. The polarization characteristics of the beam are therefore of interest. In this letter, we discuss some considerations in SHG microscopy of collagen when the incoming beam is circularly polarized, and present some supporting results as well as a numerical analysis. We propose a quasi-crystal model of collagen microstructure in an effort to further our understanding on this protein.