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The advantages of quantitative ultramorphological (QUM) sperm analysis in the diagnosis and treatment of male infertility are presented. QUM methodology is based on three elements: (1) complementary SEM and TEM observations of 7 sperm cell subcellular organelles: acrosome, postacrosomal lamina, nucleus, neck, axoneme, mitochondrial sheath, and outer dense fibers; (2) systematic classification of the specific ultramorphological malformations into 4 pathological and the normal categories, which indicate the morphological state of each subcellular organelle; and (3) comparison between well-defined reference groups with opposite fertility status or treatment conditions. QUM analysis has enabled the establishment of two indices that optimally express the in vivo and in vitro male fertility potential: The Natural Fertility Index (NFI), which allowed an accurate prediction (97% sensitivity and 90% specificity) of 80% of the naturally fertile and suspected infertile male patients, and the in vitro fertilization (IVF) score, which enabled prediction of 76% of the nonfertilizing and 90% of the fertilizing IVF groups. Validation tests confirmed these data. QUM also enabled assessment of ultramorphological indications for varicocele and radiation exposure: Both male factor etiologies indicated a persistent effect on the natural fertility potential, as expressed by structural changes in the nucleus. Varicocele was found to cause defects in the sperm head organelles related to early spermatid development, whereas ionizing radiation resulted in amorphous head shape. Criteria for specific non-in vitro therapeutic interventions such as varicocelectomy, follicle-stimulating hormone (FSH) administration, and acupuncture treatment were established. A varicocele index, which enabled the correct classification of 79 and 89% of the patients pre- and post-high ligation, respectively, was suggested to be a good indicator for varicocele which affects the fertility potential. Males exhibiting idiopathic impairment of sperm acrosome and nucleus were found to be potential responders to FSH treatment, whereas patients exhibiting low sperm activity proved to be good candidates for acupuncture treatment. Indications for selecting the optimal appropriate assisted reproduction technique (ART) procedure were found: Patients with a low Natural Fertility Index should be recommended for ART. A first choice ART selection should be performed according to an ART index based on the ultramorphological examination of the tail axoneme. The above index enabled correct prediction of 78% of the patients who achieved pregnancy following conventional ART (intrauterine insemination or IVF) and 74% of those whose wives conceived only following intracytoplasmic sperm injection. QUM sperm analysis is clinically informative, nontraumatic, and in the long run also cost-effective. This analysis should be performed when the male infertility factor cannot be clearly diagnosed by routine tests and prior to the first ART trial.