Background: Failure to thrive is one of the most important health problems of children around the word and in developing countries. This study aimed at investigating factors associated with failure to thrive among the children aged 3 to 72 months in Jahrom city of southern Iran. Methods: This case-control study comprised of 250 children aged 3 to 72 months. The case group included children with growth curves below the third percentile in more than one measurement and children above the third percentile with failure to gain weight or with weight loss during at least 1 month. The control group was selected from children with normal growth rate. The case and control groups were matched in terms of age and gender. The chi-square test and logistic regression method were applied for analysis of data using the SPSS 17 software. Results: Failure to thrive in children was significantly associated with factors, such as lower level of mother's education (OR = 4.29, %95 CI = 1.80 -10.25, P < 0.001), mother's body mass index being less than 18.5 before pregnancy (OR = 22.06, %95CI = 4.83 -100.73, P < 0.001), parental consanguinity (OR = 2.02, %95CI = 1.081 -3.79, P = 0.028), and bottle feeding (OR = 2.72, %95CI = 1.34 -5.34, P = 0.005). Conclusion: Failure to thrive causes serious complications in children later in their lives. With regards to the relatively high prevalence of this problem among children aged under 6 years of age, it is therefore deemed necessary, as an important health problem, to identify factors associated with this disorder, improve pre-pregnancy care, promote women's education level, and train parents to consider appropriate nutrition of children and healthy pregnancy.