The formation of different types of the artifacts in the amplification reaction with using different classes of the molecular-genetic markers (Indel and SSR) was studied. It was shown that DNA heteroduplexes formed during amplification of heterozygous samples, as fragments of target genes and microsatellite loci. During the electrophoresis in native polyacrylamide gel of the amplification products of homozygous samples for microsatellite loci it was revealed specific additional fragments that do not belong to the class of heteroduplex DNA. It was supposed, that the additional fragments belong to a special type of homoduplex DNA – non-linear homoduplexes. The analysis revealed that the formation of a non-linear homoduplex DNA takes place on the 20–25 cycle of the PCR, both at the amplification of the individual samples, and individual DNA fragments that was cut out from the gel.