Abstract Study question What are the specific changes under gender affirming hormone therapy (GAHT) in the spermatogonial cell compartment in testicular tissues of transwomen? Summary answer GAHT has a negative effect on the most undifferentiated PIWIL4+ spermatogonia potentially leading to reduced chances for fertility preservation in transwomen. What is known already Transwomen take GAHT to achieve transition between the gender assigned at birth and their gender identity. GAHT leads to a reduction of the most advanced germ cells and a reduction of MAGEA4 positive spermatogonia (pan spermatogonial marker). Single-cell RNA sequencing studies identified spermatogonial subpopulations based on the expression of the marker genes PIWIL4, FGFR3, NANOS3, GFRA1, KIT, UTF1. PIWIL4+ cells are considered the origin of germ cell differentiation (state 0). State 1 and 2 spermatogonia are characterized by expression of GFRA1 and KIT, respectively. Study design, size, duration On the day of gender affirming surgery (GAS) testicular tissues and blood samples were collected of 25 age matched trans women (mean 28.1 yr), who underwent comparable GAHT regimens (10 or 12.5 mg cyproterone acetate and estrogens) between 2013 and 2018. 8 adult cis men (mean 34.5 yr) with complete spermatogenesis served as controls. Age, start and type of GAHT were assessed using a questionnaire. This study was approved by the local ethics committee. Participants/materials, setting, methods We performed immunohistochemical stainings to evaluate the expression of spermatogonial markers (MAGEA4, UTF1, PIWIL4, FGFR3, NANOS3, GFRA1) in Bouin’s-fixed testicular tissue sections. For each marker the number of positive cells per round tubular cross-section was determined in 25 round tubules. The spermatogonial proliferation rate was evaluated using immunofluorescence co-stainings for GFRA1/MIKI67/MAGEA4 and KIT/MKI67/MAGEA4. We scored 400 MAGEA4+ cells per individual and determined the proportion of GFRA1+/KIT+. MKI67+ cells among the GFRA1+/KIT+ were evaluated. Main results and the role of chance The number of MAGEA4+ spermatogonia and the proportion of PIWIL4+ spermatogonia within the MAGEA4+ spermatogonia were reduced in transwomen compared to controls (p < 0.001). In contrast, the relative proportion of UTF1+, FGFR3+ and NANOS3+ spermatogonia was comparable. The number of spermatogonia per tubule correlated negatively with the age at start of GAHT (p < 0.01) and the age on the day of GAS (p < 0.001). The treatment duration correlated negatively with the proportion of PIWIL4+ (p < 0.01) and NANOS3+ spermatogonia (p < 0.05). The immunofluorescence stainings in transwomen revealed a similar ratio of proliferating KI67+ spermatogonia, both within the GFRA1+ and KIT+ cells, compared to controls. These results show the negative effects of the GAHT itself on the population of spermatogonia as well as the individual susceptibility depending on age-related factors. These results have the potential to better define the chances for fertility preservation under GAHT. Limitations, reasons for caution Transwomen are a very heterogeneous patient group varying in age, different GAHT, different treatment durations, intake of co-medications and possible pre-existing medical conditions. Hence, testicular size and histological appearance of transwomen’s testes are heterogeneous. Wider implications of the findings Transwomen, who wish to have own biological children, have to be counseled with regard to fertility preservation, best before initiation of GAHT, in order to avoid adverse effects on spermatogonia. Individual counselling has to take place with regard to fertility preservation. Trial registration number 2012-555-f-S