Grapevine (Vitis vinifera L.) is one of the classical fruits of the Old World. Among the thousands of domesticated grapevine varieties and variable wild sylvestris populations, the range of variation in pip morphology is very wide. In this study we scanned representative samples of grape pip populations, in an attempt to probe the possibility of using the 3D tool for grape variety identification. The scanning was followed by mathematical and statistical analysis using innovative algorithms from the field of computer sciences. Using selected Fourier coefficients, a very clear separation was obtained between most of the varieties, with only very few overlaps. These results show that this method enables the separation between different Vitis vinifera varieties. Interestingly, when using the 3D approach to analyze couples of varieties, considered synonyms by the standard 22 SSR analysis approach, we found that the varieties in two of the considered synonym couples were clearly separated by the morphological analysis. This work, therefore, suggests a new systematic tool for high resolution variety discrimination.