The benefit assessment of new drugs in Germany requires the submission of a value dossier including systematic searches. The majority of dossiers are methodically inspected and assessed by the German Institute for Quality and Efficiency in Healthcare (IQWiG). The study’s objective was the analysis of common deficiencies in systematic searches and their consequences for the IQWiG assessment. A total of 37 IQWiG assessment reports were analysed with regard to all comments made on the presented systematic searches in the dossier of the pharmaceutical company. A distinction was made between literature and study searches. The respective IQWiG comments were categorized and listed. Inadequate searches were examined in terms of consequences for the assessment by the IQWiG. Consequences were divided into those affecting the search required for the substance itself and those carried out for indirect comparisons/ further investigations. A total of 4 of the 37 dossiers passed the IQWiG assessment without deficiencies. Out of all analysed searches a total of 104 deficiencies were found, of which the most frequent ones referred to the search strings (32%) and the documentation of the search (25%). In the consistency check on the number of hits deviations were found by the IQWiG in 13%; 92% of the inconsistencies occurred in study-registry versus 8% in literature searches. There were no consequences in 62% (23/37) for the substance-search and in 22% (8/37) for indirect comparisons/ further investigations. Non-consideration of study results, which was the most frequent consequence of an inadequate search, occurred in 24% for the substance-search and in 32% for indirect comparisons/further analyses. The methodological requirements for systematic searches to be accepted by the IQWiG are not achieved in the majority of dossiers. An adequate design and a careful documentation of the searches is crucial to ensure the best possible acceptance of evidence in the AMNOG process.