Three computer programs for designing alternative primers for MS-PCR were tested using both default and user-defined settings. The three primer design programs used in the study were MethPrimer, Primo MSP 3.4 and Methyl Primer Express Software v1.0. In each program, a DNA sequence is entered as the starting material. Then the program searches the sequence for potential CpG islands. Next, the primers are selected around the potential CpG islands designated by the user. The results of the primer selection are delivered through a web browser as text and a graphic preview. The programs use different algorithms, which results in the detection of different numbers and lengths of CpG islands. MethPrimer was the easiest to use and the most effective. Methyl Primer Express was also effective, but this is a program for at least moderately advanced users. An advantage of Methyl Primer Express and Primo MSP is their ability to analyse an entire genome without splitting it into fragments. MethPrimer has been used with its default settings in cancer research and in research on transgenic animals. Methyl Primer Express software has been widely used in basic research, as well as in research on the regulation of gene expression and in cancer research. MethPrimer and Methyl Primer Express can be recommended for research on honey bees.