The majority of rat problems in cities are thought to be related to defective sewers, and the use of anticoagulant rodenticides in such places is often implemented as part of regular urban rodent control. Knowledge pertaining to the resistance status of sewer rat populations is non-existent, which may be leading to control problems in cities. It has become crucial to provide knowledge on the prevalence of resistance and how different control strategies have affected its prevalence among sewer rat populations. The prevalence of resistance was investigated in six sewer locations in Copenhagen and its suburban area by means of the blood clotting response (BCR) test and amplification refractory mutation system polymerase chain reaction (ARMS PCR) analysis, and by additional sequencing of the VKORC1 gene. The sewer locations were chosen to represent three different control strategies: (i) no anticoagulant use for approximately 20 years; (ii) no anticoagulant use for the last 5 years; (iii) continuous use for several decades up to the present. A low level of anticoagulant resistance was found in the sewers regardless of control strategy. Surprisingly, none of the rats, including the resistant rats, had resistance-related mutations in the VKORC1 gene. The results of this study suggest that the genetic background of anticoagulant resistance may have to be redefined in respect of resistance-related changes in the VKORC1 gene.