Introduction In Germany vaccination recommendations are revised annually and published by the Standing Committee on Vaccination at the Robert Koch Institute (STIKO). In 2010 the vaccination recommendations were amended to include the proposal that pregnant women in the 2nd trimester of pregnancy and pregnant women with additional underlying disease in the 1st trimester of pregnancy should be vaccinated against seasonal influenza. This paper reports on vaccination rates and the factors influencing them. Method A cross-sectional study was carried out in two level 1 perinatal centers in two different German federal states (Saarland and Rhineland-Palatinate) during the influenza seasons of 2012/2013 and 2013/2014. A total of 253 pregnant women were included in the study. Pregnant women were interviewed using a standardized, pre-tested questionnaire and asked whether they were aware of the recommendation to vaccinate against seasonal influenza and about possible factors which might influence their decision to be vaccinated. In addition, data from their vaccination certificates and pregnancy passports were evaluated. Results Overall, the records of only 19.5 % of the pregnant women showed that they had been vaccinated against influenza in pregnancy. Among the group of pregnant women who had a previous history of vaccinations against influenza the willingness to be vaccinated was high (43.3 %) and this figure was statistically significant. The vaccination rate was even higher (49.9 %) and even more statistically significant among pregnant women whose gynecologist or family physician had recommended that they should be vaccinated. In contrast, only 3.3 % of pregnant women who had not been given the recommendation to vaccinate by their physicians were vaccinated against influenza. Discussion The failure to recommend that pregnant women be vaccinated against influenza and women's lack of any previous experience of influenza vaccination were the main reasons for the inadequate influenza vaccination coverage in pregnancy. Conclusion One of the key points to increase the influenza vaccination rate is to intensify the counselling of the pregnant women through the gynecologist.