Deuterated crystals of l-threonine have been grown by slow cooling technique. The grown crystals were subjected to XRD, FTIR, UV–vis–NIR and thermal analyses. Isotopic exchange of protons of in NH and OH sites of l-threonine has been confirmed from the Fourier transform infrared spectroscopy (FTIR). Transmission range of the crystal was determined by UV–vis–NIR spectra. The thermal stability of the crystal was determined by differential scanning calorimetry (DSC). Dielectric measurements were carried out on deuterated l-threonine single crystals at room temperature. The dielectric constant of deuterated crystal remains constant for the entire frequency range studied. The powder SHG efficiency of the deuterated salt was found to be 0.91 times that of KDP. The results have been discussed in detail.