A panel of horse-mouse heterohybridoma cells was tested for genetic markers using biochemical and polymerase chain reaction-(PCR-) based tests. Biochemical markers included phosphoglucomutase (PGM), glucose phosphate isomerase (GPI) and 6-phosphogluconate dehydrogenase (PGD). Markers detected using PCR-based tests included microsatellite markers HTG2-15, HMS 1-3, 5-8, VHL20, ECA2 and genes for equine major histocompatibility gene ELA-DRA, tumour necrosis factor alpha (TNFA) and transferrin. The results were analysed for correlation and concordance. Based on the results, five synteny groups were identified, specifically between ELA-DRA, TNFA, HMS5 and HTG5; between HTG3 and HTG13; between HTG4, HTG8 and HMS3; between HTG6 and HMS1; and between HTG7, HTG9 and HMS6. Evidence was also found for synteny between HTG12, HMS7 and ECA2, however, confirmation requires further testing. Cytogenetic evaluation of the cell lines making up the panel indicated that large metacentric chromosomes were preferentially lost or tended to break at the centromere. Consequently, the results from this analysis can be used to identify synteny, but not to exclude synteny.