Background: Congenital hypothyroidism is one of the most common preventable causes of mental retardation. The present study aimed to compare the characteristics of neonates with false-positive congenital hypothyroidism screening test results with affected neonates in Kerman. Methods: This cross-sectional study was conducted on neonates called to confirm congenital hypothyroidism from 2016 to 2017. The neonate characteristics (year and season of birth, sex, umbilical hernia, fontanelle conditions, constipation, jaundice, abnormalities, head circumference, height and weight at birth, gestational age, type of delivery, parental consanguinity, history of thyroid disease in the family, childbirth location, history of hospitalization, and place of residence) and maternal characteristics (age, number of deliveries, history of stillbirth, history of illness, and drug use during pregnancy) were extracted from their medical records. The collected data were analyzed with SPSS software (version 20) using the chi-square and independent samples t test. Results: From a total of 985 neonates who had a positive screening test, congenital hypothyroidism was confirmed in only 58 neonates(5.9%), and the other 927 neonates(94.1%) only had a positive screening test. The neonates’ and mothers’ characteristics were not significantly different in the two groups, except for constipation, which had a higher frequency in the neonates with a positive congenital hypothyroidism screening results than in the affected neonates (P=0.004). Conclusion: In this study, the characteristics of neonates who only had a positive hypothyroidism screening test result were not significantly different from those of the affected neonates. It is recommended that further studies be conducted over a longer period.