Background: Inborn errors of metabolism (IEM) are disorders in which there is a block at some point in the normal metabolic pathway caused by a genetic defect of a specific enzyme. Diagnosis is important not only for treatment and prognostication but also for genetic counseling and antenatal diagnosis in subsequent pregnancies. Objective: The present study aimed to find out the relative frequency of inborn errors of metabolism among infants with unapparent cause of failure to thrive (FTT). Patients and Methods: This study was cross-sectional prospective study, which was conducted during the period from 2017 to August 2019. It included 58 cases with non-apparent cause of failure to thrive admitted at Pediatric Department, Faculty of Medicine, Zagazig University. All studied cases were subjected to: EMS (extended metabolic screen) using filter paper by Tandem Mass Spectrometry. Urinary organic acids analysis was performed. Results: In this study, frequency of inborn errors of metabolism (IEM) among the studied unapparent causes of FTT cases was 8.6%. Types of IEM diseases among the studied cases were one case for each of biotinidase enzyme deficiency (1.7%), methyl malonic acidemia (1.7%), mitochondrial disease (1.7%), organic acidemia (1.7%) and phenylketonuria (1.7%). There was statistically significant increase in complains of vomiting and diarrhea among cases with inborn errors of metabolism than those without inborn errors of metabolism. Conclusion: There was high frequency of inborn errors of metabolism (IEM) among FTT without apparent cause. Frequency of hypoglycemia, positive ketone in urine, high anion gap and high serum ammonia were significantly more frequent among cases with inborn errors of metabolism than those without inborn errors of metabolism.