MLPA facilitates the amplification and detection of multiple targets with a single primer pair. In a standard multiplex PCR reaction, each fragment needs a unique amplifying primer pair. These primers being present in a large quantity result in various problems such as dimerization and false priming. With MLPA, amplification of probes can be achieved. Thus, many sequences (up to 40) can be amplified and quantified using just a single primer pair.  MLPA reaction is fast, inexpensive and very simple to perform.
MLPA has a variety of applications including detection of mutations and single nucleotide polymorphisms, analysis of DNA methylation, relative mRNA quantification, chromosomal characterisation of cell lines and tissue samples, detection of gene copy number, detection of duplications and deletions in human cancer predisposition genes such as BRCA1,  BRCA2, hMLH1 and hMSH2 and aneuploidy determination. MLPA has potential application in prenatal diagnosis both invasive and noninvasive. 
Recent studies have shown that MLPA (as well as another variants such as iMLPA) is a robust technique for inversion characterisation.