During early testicular development, neonatal gonocytes transform into spermatogonial stem cells (SSC), and any untransformed gonocytes are thought to undergo apoptosis. In human cryptorchidism, persisting gonocytes may lead to seminoma. Using Bcl2-associated X knockout (BAXKO) mice, we investigated apoptosis in gonocyte development during mouse minipuberty. Testes from BAXKO, heterozygous (HET), and wild-type (WT) littermates were collected on postnatal days 1, 3, 6, and 9 (<i>n</i> = 6/group), labelled with antibodies against mouse vasa homologue (MVH, germ cell marker) or promyelocytic leukaemia zinc-factor (PLZF, SSC marker) and imaged for cell counting. Total germ cells/tubule, i.e., the number of germ cells on and off the basement membrane (BM), were counted using Image J followed by 2-way ANOVA analysis with Prism. Total PLZF+ germ cells/tubule, PLZF+ germ cells/tubule off BM, total MVH+ germ cells/tubule, and MVH+ germ cells off BM/tubule were significantly higher at day 9 in BAXKO compared to WT and HET mice (<i>p </i>< 0.01). In conclusion, knockout of BAX in mouse leads to gonocytes persisting at the centre of the tubules after minipuberty, which failed to migrate and transform into SSC, indicating the important role of apoptosis is to eliminate undifferentiated gonocytes during transformation. Failed apoptosis in gonocytes may be the cause of malignancy in humans with cryptorchidism.