The presence o f B chromosomes in the yellow-necked mouse Apodemus flavicollis (Melchior, 1834) was analyzed in 320 adult animals from four localities in Yugoslavia. Our aim was to assess the effects of B chromosomes on certain morphometric charac teristics. The characters that were chosen are included in the taxonomic discrimination o f this particular species as well as the sibling species Apodemus sylvaticus (Linnaeus, 1758). B chromosomes were found in all the localities with frequencies ranging from 21.6% to 42.9%. It was ascertained that different frequencies o f animals with B chromo somes change the slope o f the regression curve o f the length o f foramina incisiva (FI) relative to the distance from the 3rd upper molar to the incisor (IM3). This finding questions the validity of use o f this relative value in taxonomy without taking into consideration karyological data. It was also established that the relative length o f the tail (the body/tail ratio) significantly increase in the presence of B chromosomes. As this index demonstrates significant geographic variability the result could be taken as a trend only.