Background/aim: Biotinidase deficiency (BTD) is characterized by broad genotypic variants and unsteady biotinidase activity. Increasing enzyme activity and maturation throughout childhood. This study aims to reveal the course of biotinidase activities in a long-term follow-up period and concordance with their genotypes .Participants/Methods: A total of 1,773 biotinidase enzyme (BT) activity measurements were performed in 711 newborns with variants in the BTD gene over a 4-year follow-up period. Biochemical phenotyping was classified into four groups based on the highest measured enzyme activity level during the follow-up: Profound(≤10%), Partial(10.1-30%), Heterozygous(30.1-66.5%), and Normal(>66.6%). Results: The number of participants with BTD in the biochemical phenotype groups assigned based on the first measurement was 59, 217, 314, and 121 in the profound, partial, heterozygous, and normal groups respectively. Based on the highest measurement value during follow-up, the number and net changes of participants in groups were 22(-37), 95(-122), 333(+19), and 261(+140), respectively. The overall concordance between genotypes and biotinidase activities based on the highest measurement was 50.7%. A moderate correlation was found between the highest enzyme value and age (r=-0.573, p=0.002) in heterozygous plus normal biochemical phenotype groups in first months.Conclusion:This study shows that the biotinidase activities increase at a later age after neonatal period during long-term follow-up, and there is low concordance between the biochemical phenotype and their genotype. These findings indicate the important role of the monitoring the course of biotinidase enzyme activities for a longer period of time to determine the treatment decision.