Background Some evidence suggests that infertile men, who are at increased risk for hypogonadism, metabolic derangements, and osteoporosis, have higher long-term morbidity and mortality than controls, but data are scarce and not conclusive. Objective We tested whether semen quality and reproductive function could represent a marker of general male health. Design, setting, and participants A retrospective study of 5177 individuals from a prospectively collected database of 11 516 males of infertile couples who had semen analysis in a tertiary university center. Outcome measurements and statistical analysis Of them, 5177 had all data for reproductive hormones, testis ultrasound, and biochemical determinations for glucose and lipid metabolism. Hypogonadism was defined as testosterone 9.4 IU/l. Individuals with a total sperm count of Results and limitations Men with a low sperm count ( Conclusions This is the largest study with comprehensive evaluation of semen quality and reproductive function, etiology and risk factor determination, and metabolic, cardiovascular, and osteoporosis risk assessment, performed in men referred for fertility evaluation. A low sperm count is associated with poorer metabolic, cardiovascular, and bone health. Hypogonadism is mainly involved in this association, but a low sperm count in itself is a marker of general health. Patient summary This large study evaluated semen quality, reproductive function, and metabolic risk in men referred for fertility evaluation, and showed that a man’s semen count is a marker of his general health. Men with low sperm counts are more likely than those with normal sperm counts to have greater body fat, higher blood pressure, higher “bad” (low-density lipoprotein) cholesterol and triglycerides, and lower “good” (high-density lipoprotein) cholesterol. They also have a higher frequency of metabolic syndrome and insulin resistance, a condition that can lead to diabetes. Men with low sperm counts had a 12-fold increased risk of hypogonadism or low testosterone levels, and half of them had osteoporosis or low bone mass. Fertility evaluation gives men the unique opportunity for health assessment and disease prevention.