BackgroundOvarian clear cell carcinomas (OCCCs) are rare, aggressive and chemoresistant tumors. Geographical and ethnic differences in the incidence of OCCC have been reported with a higher incidence in Asiatic countries. There is a paucity of information regarding OCCC in Latin America (LA) and other countries.MethodsHere, we characterized two cohorts of 33 patients with OCCC from LA (24 from Brazil and 9 from Costa Rica) and a cohort of 27 patients from Spain. Genomic analysis was performed for 26 OCCC using the OncoScan platform. Tumors were classified according to their genomic landscapes into subgroups. Clinical parameters were related to the frequency of genomic aberrations.ResultsThe median overall survival (OS) was not significantly different between the cohorts. Genomic landscapes were characterized by different homologous recombination deficiency (HRD) levels. No difference in the distribution of genomic landscapes profiles was detected between patients from the different cohorts. OCCCs withMYC-amplified tumors harboring a concomitant loss of a region in chromosome 13q12-q13 that includes theBRCA2gene had the longest OS. In contrast, patients carrying a high number (> 30) of total copy number (CN) aberrations with no concomitant alterations inMYCandBRCA2genes presented the shortest OS. Furthermore, amplification of theASH1Lgene was also associated with a shorter OS. Initial-stage OCCCs with early progression were characterized by gains in theJNK1andMKL1genes.ConclusionsOur results provide new data from understudied OCCC populations and reveal new potential markers for OCCCs.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12885-023-11095-8.