Objectives. To describe the standardization of molecular detection and frequency of a growth hormone receptor gene deleted for exon three (GHRd3) polymorphism in a population of Peruvian children with idiopathic short stature. Materials and methods. Peripheral blood samples were used from patients (N=64) who were diagnosed with idiopathic short stature and were treated at the endocrinology unit of the National Institute of Child Health in Peru The amplification of exon 3 was carried out using G1, G2, and G3 primers by optimizing PCR conditions, such as annealing temperature and magnesium concentration. Results. The specificity of primers was maximized at 67 °C and there were no differences between magnesium concentration tests. Two-thirds (67%) of patients were GHRfl homozygous, 28% were heterozygous, and 5% were GHRd3 homozygous. Conclusions. The test was useful in determining the genotypes of patients with idiopathic short stature and revealed that only 5% had a genotype that would respond better to rhGH treatment. Thus, molecular assays may be useful when considering the decision to start drug therapy.