The present work describes the first attempt to use microwave reversed phase high performance liquid chromatography (MW-HPLC) to carry out the separation of organic compounds. Biotin and riboflavin were selected for the characterization of the new separation technique. Additional vitamins (nicotinamide, pyridoxine and thiamine) were used as reference compounds. In order to perform the separation, a chromatographic column was placed inside a domestic microwave oven in a hanging position. The column particular location was an extremely critical point, since it precluded the actual power absorbed by the sample. In order to avoid magnetron damage, a heat well (i.e., water vessels) was used. Vitamins were detected using a UV-VIS detector. Results obtained showed that the application of microwave radiation, even at low power levels, gave rise to a significant modification in the characteristics of the chromatograms. It was found that retention times for biotin and riboflavin shortened as the power increased. Furthermore, the peak shape also changed, with the modification being more significant for the former vitamin than for the latter one. Furthermore, sensitivity also increased as the column was exposed to the action of microwave. Comparatively speaking, MW-HPLC was more efficient in terms of compound separation than when performed at room temperature or thermostatted at 45 °C HPLC. This was likely due to the combined action of a moderate and quick heating of the mobile phase with an increase in the analytes diffusivity caused by the radiation.