We elucidate the crystalline nature and the three-dimensional orientation of isolated organic nanocrystals embedded in a sol-gel matrix, using a polarized nonlinear microscopy technique that combines two-photon fluorescence and second harmonic generation. This technique allows the distinction between mono-crystalline structures and nano-scale poly-crystalline aggregates responsible for incoherent second harmonic signals.PACS numbers: 78.67. Bf, 61.82.Rx The optical properties of nanoparticles have recently attracted much attention. In addition to metallic and semiconductor nanoparticles which are now used as biomarkers and as the building blocks of nanostructured materials [1], their organic counterparts constitute an interesting alternative. Advances in molecular engineering have enabled the design of molecular structures of various resonances and symmetries with optimized one-and two-photon absorption cross sections [2], or combining different optical properties such as luminescence and second harmonic generation (SHG) [3]. In addition, macroscopic molecular arrangements have been optimized using the tensorial oriented gas model [4], which predicts that an enhancement of the SHG efficiency is expected from the non-centrosymmetric crystalline arrangement of efficient nonlinear molecules. Molecular nanocrystals can be therefore envisioned as a new class of multi-functional nano-scale materials. In the case of organic nanocrystals however, the traditional crystalline characterization techniques have raised many practical barriers due to their low concentration and fragility. Consequently, the elucidation of their crystalline nature has been so far indirect or averaged over a large number of nanocrystals [5].In this letter, we show that two-photon nonlinear microscopy permits in-situ characterization of isolated organic nanocrystals grown in an amorphous sol-gel matrix. The diagnostic is based on polarization resolved two-photon excited fluorescence (TPF) and SHG. TPF is an incoherent process allowed in centrosymmetric media, which exhibits a specific anisotropy depending on the medium symmetry. On the other hand, SHG is the signature of a crystalline non-centrosymmetric phase in the sample, with a sensitivity down to the nanometric scale [6,7]. We show that the polarization analysis of both TPF and SHG from nanocrystals allows the unambiguous discrimination between isolated mono-crystalline and poly-crystalline systems. Moreover, once a nanocrystal has been identified as mono-crystalline, a detailed model for both TPF and SHG polarization responses accounting for the unit-cell symmetry allows the determination of its three-dimensional orientation within the host matrix.The organic nanocrystals that we investigate are based upon the α-((4'-methoxyphenyl)methylene)-4-nitro-benzene-acetonitrile) molecule (CMONS), which exhibits efficient luminescence and quadratic nonlinearity under two-photon excitation [8,9,10]. The bulk crystalline phases of such crystals have three possible polymorphic forms, two being noncen...