Gradient index (GRIN) lenses are often used as an optical relay to a sample at a location that is not accessible for a standard microscope. This capability is turning them into an important enabling technology that extends many optical imaging modalities like harmonic laser scanned imaging with micro endoscopic in vivo capabilities as needed in research and diagnostics. These micro endoscopic imaging variants however rely on the light scattering capability of the underlying tissue. Further complications arise from an increased number of optical interfaces and the overall optical performance of a GRIN rod. We have therefore performed a quantitative comparison of the back-scattered second harmonic generation (SHG) signal intensity generated in skin and low-scattering muscle tissue, both obtained with a standard two photon laser scanning microscope (LSM) and a GRIN lens based LSM. We report that the GRIN lens based system sees approximately 1/4 of the net two photon signal detected by the standard LSM. We expect that this value can be generalized to other LSM techniques enhanced by GRIN technology and encourage its use in experimental situations with standard LSM signal to noise ratios of four or higher.