Homozygous males show defects at multiple stages of spermatogenesis. Abnormal nuclear extensions (or 'herniations') of the nucleus are seen in primary spermatocytes at stage S3. These herniations contain chromatin and lamin. At the prometaphase stage, more than 90% of cells show aberrant chromatin condensation and variably sized chromatin fragments are also often seen. Onion stage spermatids have nuclei and Nebenkern of varying size and often contain two mislocalised centrioles per nucleus (wild-type controls contain a single centriole). Spermatids with elongated tails are seen, but the tails are disorganised and the nuclei fail to transition to the needle shape typical of wild-type elongated spermatids. The individualisation complex does not assemble and spermatogenesis arrests prior to spermatid individualisation. The seminal vesicle completely lacks mature sperm.

All meiotic cysts have at least one abnormal metaphase I or anaphase I figure in homozygous males. Metaphase I figures have fragmented and variably condensed chromatin, some of which lies outside the metaphase plate, and abnormal spindles with misplaced centrosomes are seen. Anaphase I defects include lagging chromosomes, chromatin bridges, unbalanced chromosome segregation and spindles with reduced microtubule density and misoriented microtubules. Telophase I defects include aberrantly shaped spindles with misoriented microtubules, failure to form the actomyosin band at the midzone and failure of the actomyosin band at the midzone to constrict. Meiosis II figures are not seen in the mutant testes.

Brain neuroblasts of Rae1^Z5584/Df(2R)ED3923 third instar larvae have a significantly higher mitotic index and lower frequency of anaphase configurations compared to wild type. Brain neuroblasts of Rae1^Z5584 homozygotes have a significantly lower frequency of anaphase configurations compared to wild type, but the mitotic index is normal.