Long-term musical expertise has been shown to be associated with a number of functional and structural brain changes, making it an attractive model for investigating use-dependent plasticity in humans. Physiological interhemispheric inhibition (IHI) as examined by transcranial magnetic stimulation has been shown to be correlated with anatomical properties of the corpus callosum as indexed by fractional anisotropy (FA). However, whether or not IHI or the relationship between IHI and FA in the corpus callosum can be modified by different musical training regimes remains largely unknown. We investigated this question in musicians with different requirements for bimanual finger movements (piano and string players) and non-expert controls. IHI values were generally higher in musicians, but differed significantly from non-musicians only in string players. IHI was correlated with FA in the posterior midbody of the corpus callosum across all participants. Interestingly, subsequent analyses revealed that this relationship may indeed be modulated by different musical training regimes. Crucially, while string players had greater IHI than non-musicians and showed a positive structure-function relationship, the amount of IHI in pianists was comparable to that of non-musicians and there was no significant structure-function relationship. Our findings indicate instrument specific use-dependent plasticity in both functional (IHI) and structural (FA) connectivity of motor related brain regions in musicians.