For many years, endometriosis has been an enigmatic and confusing disorder, but there have been recent contributions to the subject, provided by modern techniques in cellular and molecular biology, regarding the cell lineage involved, the stage of differentiation, and genomic features. This review deals mainly with the cellular, cytochemical, cytogenetic, and molecular cytogenetic features of primary endometriotic lesions and cultured endometriotic cells. The FbEM-1 cell line, taken as an in vitro model, showed cell proliferation and differentiation features suggesting an immature endometriosis-related cell lineage. Chromosomal analysis of these cells demonstrate a complex karyotype including a rearrangement interpreted as der(5) t(5q34;6p11) indicating a clonal cell proliferation. Data of recurrent DNA sequence copy number alterations detected by the comparative genomic hybridization in a series of primary endometriotic lesions also are described. Predominant recurrent anomalies were found on chromosome 1p and 22q in 50% of the studied samples. Additional losses were seen on chromosomes 5p(33%), 6q(27%), 7p(22%), 9q(22%), and 1q(22%), as well as on 17q segments in one case. Gain of DNA sequences was seen on chromosomes 6q, 7q, and 17q. The potential role of the genetic changes identified are discussed in relation to the putative oncogenes and/or tumor suppressor genes possibly involved in development of endometriosis.