The aim of this study was to investigate and compare the dissolution and vaginal absorption characteristics of metronidazole (MTZ) and ornidazole (ONZ) vaginal suppositories. The formulations were prepared by a simple fusion method using Witepsol H15. The solubility, partitioning and dissolution characteristics of these drugs were investigated in phosphate (pH 7) and lactate buffer (pH 4.5) solutions. MTZ and ONZ were labeled with Technethium-99m (Tc-99m) and their suppositories were applied to carry out the vaginal absorption and biodistribution studies in rabbits. Scintigraphic images were collected using Sophy DST and DSX gamma cameras. The dissolution of ONZ from the vaginal suppository was slower than that of MTZ at phosphate buffer and similar in lactate buffer. 49% of the administered ONZ dose remained in the rabbit's vagina after 2 h, while this value was calculated as 38% for MTZ. Total activity calculated in uterus and urinary bladder was found as 16% and 22% for MTZ and ONZ, respectively. The biodistribution studies showed that the radioactivity of MTZ in urine and blood was higher than ONZ. The radioactivity of ONZ detected in all organs, especially in uterus, kidneys and urinary bladder, was greater than MTZ. This study determined that the two labeled 5-nitroimidazole derivatives had a high absorbability performance in vagina. MTZ to a large extent transferred to blood and ONZ gathered in lipoid tissues, due to their partition characteristics.