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In recent years, brown trout catches have been declining in many Swiss rivers. One hypothesis is that this declining catch is linked to environmental estrogens, known to have the potential to adversely affect fish reproduction. In order to assess if the reproductive health of brown trout is impaired, we sampled fish at three sites along four rivers with a well documented catch decline. These rivers are affected by inputs of treated sewage effluent. The sampling was conducted during two years; we measured plasma vitellogenin (Vtg) concentrations and surveyed gonadal histology. Analysis of plasma Vtg revealed elevated concentrations (up to 8 μg/mL) in only 10 out of 197 males. Furthermore, there were no site specific patterns to this induction. These results indicate that the exposure to estrogenic compounds is low. Also the incidence of ovarian atresia was low and we found no male intersex fish. In contrast to males, females caught along two rivers had spermatogenic activity in ovarian tissue. However, this intersex condition does not appear to be connected to exposure to environmental estrogens. At one of 12 sites there was a high incidence of gonadal parasites in ovarian tissue, which may affect reproductive output but was not a general problem across sites. In conclusion, the exposure to estrogenic compounds does not appear to significantly affect the reproductive parameters we investigated in Swiss brown trout.