Non-linear optical techniques are increasingly used for investigating biological phenomena. These techniques allow ultra-deep imaging in tissues with low photo-toxicity. In this talk, I will first present two photon excitation fluorescence (TPEF) microscopy and discuss its optical performances and limitations in imaging depth due to out-of-focus signal; I will detail one possible development based on wave-front shaping with a deformable mirror to reject this background. I will also introduce coherent anti-Stokes Raman scattering (CARS) microscopy that gives access to chemical information (molecular bonds) without labeling and I will present few applications of this vibrational imaging. Its main limitation is due to the low Raman scattering cross section. However, it is possible to enhance this signal with metallic nanoparticles, it is called surface enhanced Raman spectroscopy (SERS) and it will be detailed in the second part of my talk. We particularly demonstrate that single amino acid molecule can be detected with SERS. We finally develop statistical approaches for sorting reference spectra from fluctuating data, determining the in-line molecular concentration over a wide range (from 10⁻⁶ to 10⁻¹¹ M) and investigating the protein conformations.