Abstract: Objective　To explore the clinical manifestations, diagnosis, treatment and prognosis of holocarboxylase synthetase deficiency (HLCSD) in children. Method　The clinical manifestations and laboratory tests results in a child with HLCSD were retrospectively analyzed. Genetic mutations in peripheral blood of the child and her family members were analyzed by second-generation gene sequencing. Results　The girl presented with recurrent refractory rash and the age at onset was 4 months. Humoral immunity showed a decrease in the level of total immunoglobulins. Blood tandem mass spectrometry showed a marked increase in the level of 3-hydroxy-isovalyl carnitine. Urine gas chromatography mass spectrometry showed a significant increase in lactic acid, 3-hydroxy-isovaleric acid and pyruvic acid. The second-generation gene sequencing revealed that there were heterozygous mutations of c.1544G>A (S515N) and c.1993C>T (R665X) in exon 9 and 11 of the HLCS gene in the child, and R665X was a new mutation. His parents are genetic mutation carriers. Conclusions　The clinical manifestations of HLCSD are atypical. For children having refractory rash with neurological abnormalities, growth and development disorders, persistent acidosis, hyperlactacidemia and other manifestations, HLCSD should be suspected, and the diagnosis can be confirmed early by blood tandem mass spectrometry, urine gas chromatography mass spectrometry and gene screening.