In the past, celiac disease (CD), or intolerance to gluten, was considered a rare disease of infancy characterized by chronic diarrhea with malabsorption and delayed growth. Besides the overt enteropathy, there are other clinic and subclinical forms which appear later in life. Target organs are not limited to the gut, but include liver, thyroid, skin and female and male reproductive systems. CD interference on reproduction is related to the multifactorial nature of the disease, whose pathological manifestations can be modulated, besides gluten, by different concurrent genetic and environmental factors. CD induces malabsorption with consequent deficiencies of micronutrients such as iron, folic acid and vitamin K, which are essential for organogenesis, and fat-soluble vitamins important for spermatogenesis. Regarding endocrine disorders, the deficiencies of specific trace elements on ovarian function could explain its involvement in the increased risk of female osteoporosis in CD patients. Affected males show a picture of tissue resistance to androgens; the increases of follicle-stimulating hormone and prolactin, not associated with infertility, may indicate an imbalance at hypothalamus-pituitary level, with general effects on health. Since reproductive alterations are reversible, adoption of a gluten-free diet supported by early diagnosis is important. Therefore, the detection of early biomarkers, such as deficiencies of vitamins and/or iron and andrological or endocrinological dysfunctions, should trigger timely strategies for prevention and treatment.