Introduction Sperm quality impairment, testis cancer and congenital malformations of the male urinary tract (cryptorchidism, hypospadias) compose the testicular dysgenesis syndrome (TDS), which is suspected to be causally linked with early/prenatal exposure to endocrine disruptor chemicals (EDCs). In the context of the growing ubiquitous exposure to EDCs in France since the 50’s, we analyzed nationwide temporal and spatial trends of TDS indicators using existing databases. Methods The national ART register (FIVNAT) provided data to study semen characteristics in France between 1989 and 2005. We analyzed three semen quality indicators from a sample of men partners of infertile women (bilateral fully blocked/absent tubes), therefore close to the general population. The French National Hospital Discharge Data Base (PMSI) provided data to study indicators of testis cancer, cryptorchidism, and hypospadias from 2002 to 2014, using diagnosis codes based on international classification of diseases, 10th revision. For each set of data, we selected the best-suited statistical model, based on Akaike or Deviance Information criteria, to describe temporal, spatial and spatiotemporal trends. Trend for each analysis was assessed by a spline function to capture potential non-monotonic relationship with TDS indicators, when spatial correlations were captured by a Besag, York and Mollie model. Results Temporal trends show a nationwide continuous impairment of male reproductive health: in 1989-2005 for sperm concentration and sperm morphology; and, in 2002-2014, for testis cancer and cryptorchidism. No trend is observed for hypospadias between 2002 and 2014. Spatial variations are observed within all these indicators. Conclusions We analyzed TDS trends for the first time at the country level. Temporal trends are globally consistent, and could be due, among possibilities, to the growing EDC exposure. All TDS indicators present strong spatial pattern but heterogeneous between them.