This study establishes a correlation between exposure and clinical alterations in the hypothalamic-pituitary-thyroid axis. Different dosages were applied, from the accepted safe dosage up to a significant increase dosage. The study was carried out under the laboratory animal center conditions at Universidad of Boyacá (Colombia). Due that ammonium perchlorate is one of the most used compounds as pesticide in Boyacá department this type of studies are extremely important. Using enzyme immunoassay in micro-plate (Accubind Elisa Microwells TSH and Kit Accubind Elisa Microwells T4L ) and following clinical analysis alterations in the hormonal axis were found which could be be indicative of a possible high risk in the future for individuals who handle this substance.