Non-destructive and high throughput methods have been developed for seed quality evaluation. The aim of this study was to relate parameters obtained from the free and automated analysis of digital radiographs of hybrid melons’ seeds to their seeds’ physiological potential. Seeds of three hybrid melon (Cucumis melo L.) cultivars from commercial lot samples were used. Radiographic images of the seeds were obtained, from which area, perimeter, circularity, relative density, integrated density and seed filling measurements were generated by means of a macro (PhenoXray) developed for ImageJ® software. After the X-ray test, seed samples were submitted to the germination test, from which variables related to the physiological quality of the seeds were obtained. Variability between lots was observed for both physical and physiological characteristics. Results showed that the use of the PhenoXray macro allows large-scale phenotyping of seed radiographs in a simple, fast, consistent and completely free way. The methodology is efficient in obtaining morphometric and tissue integrity data of melon seeds and the generated parameters are closely related to physiological attributes of seed quality.