The period in which Jews were first associated with Cochin and the Malabar coast was by tradition, after the destruction of the First Temple (586 BCE). Yet, the earliest evidence of Jewish settlements is from the tenth century CE. The largest group of Cochin Jews are the "Black Jews," of whom about 4,000 live in Israel. A high frequency of consanguineous marriages prevailed among Cochin Jews. Their mean height and weight were low when they came to Israel in 1954; an increase in both was observed 20 years later. Some of the allele frequencies of blood groups, isoenzymes, and HLA antigens were similar to those in other Jewish communities. In the high O, M, cde, and HLA-A28 and the low cDE allele frequencies Cochin Jews resembled Yemenite Jews. A few allele frequencies, the high Fya, AK2 and the low Jka and Hp1, were similar to those observed in indigenous southern Indian populations. In most HLA antigen and haplotype frequencies the Cochin Jews showed a distribution similar to that observed in other Jews and Caucasoids. No comparable HLA data on southern Indian populations were available. The results indicate that Cochin Jews have similarities with Jews, in particular Yemenite Jews, and with the indigenous populations of southern India.