Testicular germ cell tumours (TGCTs) of young adult men, seminoma (SE) and nonseminoma (NS), develop from a precursor cell, carcinoma in situ (CIS), which resembles foetal gonocytes and retains embryonic pluripotency. We used microarrays to analyse microRNA (miRNA) expression in 12 human testis samples with CIS cells and compared it to the miRNA expression profiles of normal adult testis, testis with Sertoli-cell-only (SCO) that lack germ cells, testis tumours (SE and embryonal carcinoma (EC), an undifferentiated component of NS) and foetal male and female gonads. Principal component analysis revealed distinct miRNA expression profiles characteristic for each of the different tissue types. We identified several miRNAs that were unique to testis with CIS cells, foetal gonads, and testis tumours. These included miRNAs from the hsa-miR-371~373 and -302~367 clusters that have previously been reported in germ cell tumours and three miRNAs (hsa-miR-96, -141 and -200c) that were also expressed in human epididymis. We found several miRNAs that were upregulated in testis tumours: hsa-miR-9, -105 and the hsa-miR-182~183~96 cluster were highly expressed in SE, while the hsa-miR-515~526 cluster was high in EC. We conclude that miRNA expression profile changes during testis development and that the miRNA profile of adult testis with CIS cells shares characteristic similarities with the expression in foetal gonocytes.