The nutritional iodine deficiency disorders are still a major health problem in industrialized countries, but they are completely preventable by means of iodine prophylaxis. Iodine is essential for thyroid hormone (TH) synthesis and TH is required for normal brain development. Gestational iodine supplementation may improve infant cognitive development. In this study we aimed at evaluating the intelligence quotient of children born to mothers with different levels of iodine supplementation, with or without the administration of levothyroxine (LT4), prior to and during pregnancy. In particular we focused our attention on some mother–child pairs and we compared them according to iodized salt consumption and LT4 treatment. In this specific context, NPC test was applied to compare four groups of children, defined on the basis of maternal history related to iodized salt consumption and LT4 treatment. The results show that the deficit in functionality cognitive (in terms of intelligence quotient) is significantly higher in the children of mothers that does not make supplementation of iodized salt. This shows how a lack of iodine can hinder children in reaching their full intellectual potential. From a methodological point of view, our research showed the utility of the Non Parametric Combination test (NPC test) into analyze data concerning medical research.