Y-chromosomes evolved independently many times and are a major biological phenomenon. Important questions about their origin and evolution remain unanswered, and Drosophila is a privileged model to study them. We highlight two of them. (i) Gene loss is known to play an important role on the evolution of Y chromosomes. The recent sequencing of 12 Drosophila genomes allowed a detailed study of this process. We found seven gene gains and two gene losses among the Y-chromosomes of the 12 sequenced species. The rate of gene gain is 11 times higher than the rate of gene loss (P < 0.003), which strongly suggests that the gene content of the Drosophila Y is increasing. (ii) Although it is certain that Y chromosomes usually arise from the degeneration of X chromosomes, it is possible that there are alternative pathways. Our previous finding that none of the genes of the D. melanogaster Y are shared with the X is somewhat at odds with the hypothesis that the Drosophila Y was derived from the X. We also found before that the ancestral Drosophila Y became part of an autosome in the D. pseudoobscura lineage, and was replaced by a new Y chromosome (possibly derived from a neo-Y). We are investigating how frequent this phenomenon of wholesale replacement is by studying the Y-linked gene content of a large number of Drosophila species. Among the 310 tested species, 42 had their Y chromosomes replaced, owing to four independent events (the D. pseudoobscura lineage case, and three additional lineages). None of the three additional events (amounting to 34 species) has a X-autosome fusion, so the current Y of these species cannot be a degenerated neo-Y. We conclude that gene gains and wholesale replacements play important roles in the evolution of the Drosophila Y, and hence this chromosome does not seem to fit the standard view that Y chromosomes are little more than decaying X chromosomes.