Background: Since the identification ofBRCA germline mutation, there have been no major breast cancer susceptibility genes that discovered by linkage analysis.Based on set of criteria including early age of onset and family history,the BRCA1 mutation of affected Javanesse origin with criteria set, however, are mostly unidentified.This has attributed to the heterogenious genetic basic for the hereditary susceptibility breast cancer under study.Objective: This preliminary study was aimed to find other breast cancer susceptibility genes in a breast cancer family of Javanese origin who showed no typical pathogenic BRCA1 or BRCA2 gene mutation.Method: A medium-size family of breast cancers was analyzed in this study, consisting four siblings and one niece.The entire coding sequences of BRCA1 and BRCA2 genes were investigated by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DDGE) followed by sequencing.Linkage analysis was performed by using Genemapper software with 400 DNA repeat markers.Result:A family consisting 5 breast cancer patients from Yogyakarta was analyzed.Blood samples were taken from 12 family members (male and female) in the first-degree and second-degree relatives.The strongest evidence of linkage (LOD score almost 2) was obtained on chromosomal region 3 and 4 that potentially harbouring susceptibility genes.Conclusion: This is the first study to explore the possibility of breast cancer susceptibility genes other than BRCA1 and BRCA2 in Indonesian population.Linkage analysis of a Javanese family showed a potential of breast cancer susceptibility genes in chromosome 3 and 4.