Objective: To explore the cause of discrepancy in results of thrombin time(TT) between two kinds of thrombolyzer in a 4-year-old male child with glandular hypertrophy. Methods: A series of plasma samples were obtained during 7 months follow-up periods, one stage clotting assay was used for coagulation factors tests, protamine sulfate neutralization test was performed, and three fibrinogen genes were sequenced. Results: The significant difference in TT results between thrombolyzer A (magenetic beads) and B (transmission turbidimetry) was further confirmed by two reference labs with a prolonged TT in A and normal TT in B. Activated partial thromboplastin time (APTT) were 52.4 s and 36.6 s, TT were 88.7 s and 16.7 s by A and B thrombolyzer, respectively. The prolonged TT was corrected by 50 μg/ml (final concentration) protamine sulfate, and the reptilase time was normal. No mutation was found in fibrinogen genes by gene analysis. Thus, the presence of endogenous heparin like anticoagulant in this boy was confirmed. Conclusions: Endogenous heparin like anticoagulant is rare and existed in this boy, causing the discrepancy of TT results between the two kinds of thrombokyzer. Therefore, if a discrepancy of TT results is found, other causes such as heparin like anticoagulant should be considered.