Copy number variations in the human genome are commonly detected using genome-wide high-resolution screening methods such as array-comparative genomic hybridization. To confirm these copy number variations, we have used an assay based on a semiquantitative multiplex polymerase chain reaction (PCR) of short unlabeled fragments and performed on the microfluidic Bio-Rad Experion system. We have compared the performance of this semiquantitative multiplex PCR of short unlabeled fragments assay with that of the semiquantitative multiplex PCR of short fluorescent fragments assay and have shown that its repeatability and reproducibility are very satisfying, with a relative standard deviation lower than 6.5%. We conclude that this robust and sensitive technology provides reliable data for the confirmation of rearrangements detected by array-comparative genomic hybridization.