A 32-year-old female underwent an extracapsular dissection for a pleomorphic adenoma (PA) of the parotid gland. Six months later, she presented with an increasing lump on the upper lip that, following excision, was confirmed to be a second PA. Formalin-fixed paraffin embedded tissues were analyzed for chromosomal aberrations. Comparative genomic hybridization analysis showed multiple chromosomal aberrations in the parotid PA. In comparison, no chromosomal aberrations were found in the lip PA. To our knowledge, metachronous benign pleomorphic adenomas occurring in both a major and minor salivary gland is unreported, and furthermore, there are no comparative genomic hybridization reports of this rare occurrence. We discuss the clinicopathological implications.