Due to heavy anthropogenic influence and variation of the environmental conditions in the Baltic Sea, reproductive disorders are becoming a major environmental concern. We show here an increasing prevalence of gonadal malformations in the Baltic herring (Clupea harengus membras), a key species of the Baltic ecosystem and important in commercial fishery. During 1987-2014, the spawning herring population in the Archipelago Sea (AS) (North Baltic Sea, Finland) was monitored annually and analyzed for gross morphology of the gonads [total number (n) of analyzed fish = 38 284]. Four different types of malformations were repeatedly found and named as asymmetric, rudimentary, segmented, and branched gonads, but also hermaphroditic gonads and miscellaneous (unidentified) disorders were recorded. In 2013, additional samplings (n of fish analyzed = 541) showed similar malformations in herring from the Bothnian Sea. In some gonad types, histological examination revealed disintegration of seminiferous tubules and hyperplasia of the interstitial tissue. In 2014, the overall prevalence of malformations was still relatively low in the AS (frequency = 0-3.4 %; n = 750) and had apparently minimal effect on population recruitment. However, an increasing trend in the time-series (GLM; F = 32.65; p\0.001) and a significantly higher prevalence in the Bothnian Sea (frequency = 0.7-5.0 %; n = 541; v 2 = 6.24; p\0.05) suggest that gonadal malformations may become a new threat for fish in the Baltic Sea. The observed gonad atrophies may be due to environmental endocrine disruption; however, also other explanations may exist and potential explanations are discussed.