Baltic cod, like other species, is susceptible to inter-annual fluctuations in sexual maturation, depending on the length, age, sex, extent of the habitat area, and stock abundance of the cod population. Maturity is one of the biological indicators used to detect changes in a stock that can be caused by fishing. To address these issues specifically for the eastern Baltic cod stock, long-term data (1990–2006) from Polish research vessels in the southern Baltic were examined. To date, the ICES has used the same maturity ogives over extended periods and assumed invariant sex ratios for the assessment of eastern Baltic cod. The combined maturity ogives calculated in the present study were markedly lower, particularly for age groups 2–4 (5), in all periods, than those used in the ICES assessment. Moreover, the proportion of females increased with length and age, suggesting that annual verification of the sex ratio is needed. The present study also revealed that the total length (L50%) and the age (mean age-at-maturity; MAM50%) at which 50% achieved first sexual maturity were higher for females than for males in the study period. The long-term mean L50% and MAM50% for females were 43.9 cm and 4.3 years, respectively, and for males 34.8 cm and 3.4 years. There was also a spatial difference between calculated maturity ogives, with slightly lower L50% (range: 1.4–8.6 cm) in the Gdańsk Basin than in the Bornholm Basin. The increasing trend in fishing mortality observed in 1993–2004 (ICES data) did not translate into a temporal trend in calculated maturity ogives. However, changes in L50% and MAM50% reflected recruitment variations (ICES data). The significance of these findings is discussed in the context of the environment and recruits abundance.