We report a case of primary effusion lymphoma (PEL) in a 75-year-old woman without human immunodeficiency virus or hepatitis C virus, which presented as fever, chest pain, and pericardial effusion. The lymphoma cells were positive for CD20 and CD79a, and were negative for CD3 and CD10. Genomic human herpes virus 8 (HHV-8) and Epstein-Barr virus were not detected in the lymphoma cells. Cytogenetic analysis showed complex abnormalities by the G-banding technique, and spectral karyotyping (SKY) analysis provided more detailed characterization of the chromosomal aberrations, including t(1;22)(q21;q11) and t(14;17)(q32;q23). We did not detect C-MYC gene rearrangement or BCL-2 expression. She was treated successfully with six courses of the CHOP regimen. The present case demonstrated a rare category of PEL that is not associated with HHV-8 or C-MYC gene rearrangement. In addition, SKY analysis disclosed cryptic chromosomal abnormalities involving 1q21 and 17q23.