Microsatellites are short repeating DNA sequences of two to six base pairs. The numbers of repeats can vary among individuals; they represent the different alleles. For example, allele 1 has four repeats, allele 2 has five repeats, allele 3 has six repeats, and so forth. SNPs can also be used as markers in linkage analysis; however, there are only two alleles for SNPs. For example, C/T, which means that allele 1 has C, while allele 2 has T. Due to the higher number of variability in microsatellites than in SNPs, it is easier to perform linkage analysis using microsatellites.

One of the most common examples of microsatellite is (CA)n, where n represents the number of CA repeats. The number of repeats can vary between three to 100 times, creating a high number of alleles that are present in the population. Remember that this high number of alleles is present in the population and not in the individual! We only have two copies of chromosomes meaning that we only have maximum two different alleles present in our cells. When an individual has two different alleles, for example (CA)10 and (CA)15 he/she is said to be heterozygous for the microsatellite. On the other hand, when an individual has only one allele in both the chromosomes, he/she is said to be homozygous for the microsatellite. We can analyze the genotype of the microsatellite by amplifying it using PCR and analyzing the length (the number of repeats) using gel electrophoresis.