The degradation in the quality of silver eel and their health could have been a major factor in the collapse of the European eel (Anguilla anguilla) population. However, the health status of the spawners has been poorly studied until now. This study evaluated the quality of migrant male silver eels from four Mediterranean habitats in France presenting different degrees of contamination: Canet-Saint-Nazaire, Salses-Leucate and Bages-Sigean lagoons and La Berre River. We considered pathogens including Anguillicoloides crassus and EVEX virus and the concentration of chemical contaminants including PCBs, OCs and heavy metals. Our study results revealed different patterns of pollution and infection in the four habitats, with high individual variability. No single silver eel was free of pollution. Total dichloro-diphenyl-trichloroethane (DDT) and copper contaminations, as well as the Swim bladder Degenerative Index (induced by parasitism), were remarkably high in eels from Canet lagoon, while eels from Salses lagoon showed lower levels of contaminants and parasite infection. A non-negligible proportion of eels were strongly impacted with levels of contaminants/parasites that could potentially impair their migration and reproduction. Our study revealed low to moderate contamination levels compared with the other Mediterranean sites previously reported, except for high concentrations of DDTs and Cu in Canet lagoon. We discuss the contribution of these results in the context of possible implications for silver eels reproductive success and local eel population management.