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Objective: To verify the reliability of real-time PCR for the detection of genetic mutations underlying spinal muscular atrophy (SMA) and establish quality control for clinical testing., Methods: Thirty-five patients, 61 first-degree relatives, 61 healthy controls and 7 prenatal cases which were previously genotyped by multiplex ligation-dependent probe amplification (MLPA) were tested with Roche LightCycler 480 and Bio-Rad CFX96 (TM) real-time PCR machines for relative quantification of copy number of SMN1 exon 7., Results: Genotyping detected by relative quantitative real-time PCR were consistent with the results of MLPA. Both types of real-time PCR machines could accurately distinguish different SMN1 copy numbers despite certain systematic differences between the two platforms., Conclusion: The reliability of real-time PCR assay for detecting SMA depends on quality control. Standard database generated with known SMN1 copy number variations should be established for different instruments.