In recent years, because of the constantly changing farming systems and under a limited choice of alternative crops, many farmers have been growing the same crops in the same fields for two or more consecutive years. This practice has resulted in increasing incidence and severity of take-all in winter wheat (Triticum aestivum L.) crops. The aim of this study was to evaluate the incidence and severity of take-all in winter wheat and estimate the level of Gaeumannomyces graminis var. tritici (Ggt) and G. graminis var. avenae (Gga) inoculum in the soil in three agro-ecological zones (Western, Middle Lowland and Eastern) of Lithuania. During the 2013-2014 period, takeall incidence in winter wheat varied from 2.0% to 92.0% in 81 fields inspected. The highest take-all incidence and take-all index were identified in the Middle Lowland zone, while the lowest in the Western zone. The inoculum level of Ggt/Gga in the soil was estimated using the bait method by assessing DNA amounts of pathogens in the roots of wheat plants, grown in the soil samples collected in different agro-ecological zones of Lithuania. The amounts of Ggt/Gga DNA varied considerably among the sites. Averaged data showed the lowest take-all inoculum level in Eastern zone and the highest in Middle Lowland. The highest amount of Ggt/Gga DNA was established in the samples collected in Pakruojis and Panevėžys districts. In three samples from Raseiniai, Šiauliai and Alytus districts the quantity of fungal DNA was very small 0.188-0.640 pg of fungal DNA μg-1 of plant DNA, and in five samples from Šilutė, Tauragė, Telšiai, Kėdainiai and Panevėžys districts no fungal DNA was detected. In this study, the use of different management and different environmental conditions, also unpredictability of the disease (ability to spread in patches), probably were the main reasons, which had significant impact on the marked variation of take-all incidence and severity in winter wheat crops in Lithuania.