This study was undertaken to analyze whether prolonged exposure to low-dose zearalenone (ZEN) mycotoxicosis affects the concentrations of ZEN, α-zearalenol (α-ZEL), and β-zearalenol (β-ZEL) in selected reproductive system tissues (ovaries, uterine horn—ovarian and uterine sections, and the middle part of the cervix), the hypothalamus, and pituitary gland, or the concentrations of selected steroid hormones in pre-pubertal gilts. For 42 days, gilts were administered per os different ZEN doses (MABEL dose [5 µg/kg BW], the highest NOAEL dose [10 µg/kg BW], and the lowest LOAEL dose [15 µg/kg BW]). Tissue samples were collected on days seven, twenty-one, and forty-two of exposure to ZEN (exposure days D1, D2, and D3, respectively). Blood for the analyses of estradiol and progesterone concentrations was collected in vivo on six dates at seven-day intervals (on analytical dates D1–D6). The analyses revealed that both ZEN and its metabolites were accumulated in the examined tissues. On successive analytical dates, the rate of mycotoxin accumulation in the studied tissues decreased gradually by 50% and proportionally to the administered ZEN dose. A hierarchical visualization revealed that values of the carry-over factor (CF) were highest on exposure day D2. In most groups and on most exposure days, the highest CF values were found in the middle part of the cervix, followed by the ovaries, both sections of the uterine horn, and the hypothalamus. These results suggest that ZEN, α-ZEL, and β-ZEL were deposited in all analyzed tissues despite exposure to very low ZEN doses. The presence of these undesirable compounds in the examined tissues can inhibit the somatic development of the reproductive system and compromise neuroendocrine coordination of reproductive competence in pre-pubertal gilts. View Full-Text ►▼ Show Figures This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.