The aim of this study was to develop a new male fertility diagnostic profile based on quantitative ultramorphology parameters and to determine the contribution of this profile to the enhancement of the routine semen analysis index reported previously. Semen samples from 208 males of known fertility and suspected infertility were evaluated for the ultrafine structure of the following sperm cell organelles: acrosome, post-acrosomal lamina, nucleus, neck, axonema, mitochondrial and fibrous sheaths. For each of these organelles, four pathological states (agenesis, incomplete genesis, malformation and degradation) and an intact state were defined. A quantitative ultramorphology index based on the incidence of intact nucleus, acrosome and fibrous sheath malformations enabled high accuracy in the classification (97% sensitivity and 90% specificity) of 74% of the cases. A combined semen quality index based on a proportional combination of the semen analysis and quantitative ultramorphology indices was found to increase the percentage of cases classified correctly to 80%. It was proposed that semen specimens of males whose fertility status cannot be predicted clearly using routine semen analysis should be fixed and sent for quantitative ultramorphology analysis to specialized laboratories so that their fertility potential can be determined more accurately using the semen quality index.