Female birds develop asymmetric gonads: a functional ovary develops on the left, whereas the right gonad regresses. In males, however, testes develop on both sides. We examined the distribution of germ cells using Vasa/Cvh as a marker. Expression is asymmetric in both sexes: at stage 35 the left gonad contains significantly more germ cells than the right. A similar expression pattern is seen for expression of ERNI (Ens1), a gene expressed in chick embryonic stem cells while they self-renew, but downregulated upon differentiation. Other pluripotency-associated markers (PouV/Oct3/4, Nanog and Sox2) also show asymmetric expression (more expressing cells on the left) in both sexes, but this asymmetry is at least partly due to expression in stromal cells of the developing gonad, and the pattern is different for all the genes. Therefore germ cell and pluripotency-associated genes show both sex-dependent and independent left-right asymmetry and a complex pattern of expression.