There is a clearly established relationship between masticatory muscle structure and facial form. Human studies in this area, however, have been limited, especially in consideration of the myosin heavy chain (MyHC) family of contractile proteins. The aim of this pilot study was to assess if differences were detectable between genotype with respect to MyHC isoforms and the vertical facial phenotype in a sample of nine Caucasian female patients, age range 18-49 years, using a novel rapid technique. Masseter muscle biopsies were taken from patients with a range of vertical facial form. The levels of expression of the MyHC isoform genes MYH 1, 2, 3, 6, 7, and 8 were compared with the expression in a female calibrator patient aged 23 years with normal vertical facial form, using quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) analysis. Statistical analysis was undertaken using Pearson correlation coefficient. The results showed that there were distinct differences in gene expression between patients with a wide range of variation although changes in MYH1 were consistent with one cephalometric variable, the maxillo-mandibular angle. The full procedure, from start to finish, can be completed within half a day. Rapid genotyping of patients in this way could reveal important information of relevance to treatment. This technology has potential as a diagnostic and prognostic aid when considering correction of certain malocclusions.