Objective To explore the diagnosis and treatment of primary carnitine deficiency. To identify potential mutation of SLC22A5 gene in two children affected with primary carnitine deficiency and provide genetic counseling. Methods We measured the free camitine(Co)and acylcamitine levels in a suspected clinical inherited metabolic diseases by tandem mass spectrometry. The SLC22A5 gene mutations were tested to the children with low Co level and the diagnosis was made. Then, We measured the free camitine(Co)and acylcamitine levels and SLC22A5 gene mutations in her sister. The children with PCD were treated with carnitine and followed up for 11 months. The SLC22A5 gene was detected in their family. Results In two children affected with PCD, 1 case was clinical children, another case of their sister was no obvious clinical manifestations. Mutations were found in all of them.The average C0 level in patients was lower than the reference value,along with decreased level of different acylcamitines. Two cases were treated with earnitine. Their clinical symptoms reduced 2 months later. Another case had not been sick. The CO level and different acylcamitines level in the blood rose to normal. A homozygous mutation C. 760C>T (P. Arg254X)of the SLC22A5 gene was detected in the two cases.Heterozygous mutation C. 760C>T (P.Arg254X) was also found in other family members. Conclusion Two patients were diagnosed with PCD by the test levels of free carnitine and acylcarnitines in blood with tandem mass spectrometry,and gene mutation test. L-carnitine supplement had a good effect in treatment of the PCD patients.C.760C> T (P.Arg254X) mutations of the SLC22A5 gene is the deleterious mutations for PCD families, The analysis method of the wrong mutagenesis and shear changes which is used to directly sequence the exons codes of the SLC22A5 gene can provide genetic counseling for PCD families.