Clear cell papillary renal cell carcinoma (CCP-RCC) is a recently recognized tumor that shares morphologic features of both clear cell renal cell carcinoma and papillary renal cell carcinoma but behaves in a more indolent fashion. To date, there is little molecular information available on CCP-RCC. DNA was extracted from formalin-fixed, paraffin-embedded tissue blocks of 22 cases of CCP-RCC at the University of Alabama at Birmingham. Targeted next-generation sequencing and single-nucleotide polymorphism array were performed on all cases. Next-generation sequencing analysis found 30 somatic variants across 63.3% of cases. Seventeen variants (56.7%) were predicted to be deleterious or possibly/probably damaging. Single-nucleotide polymorphism array analysis found copy number abnormalities and/or loss of heterozygosity in 22.7% of cases. We analyzed the genetic characteristics of a group of CCP-RCCs cases and found them to be genetically different from one another. Some cases were genetically similar to clear cell renal cell carcinoma.