Finger-tapping tasks have been widely adopted to investigate auditory-motor synchronization, i.e., the coupling of movement with an external auditory rhythm. However, the discrete nature of these movements usually limits their application to the study of beat perception in the context of isochronous rhythms. The purpose of the present pilot study was to test an innovative task that allows investigating bodily responses to complex, non-isochronous rhythms. A conductor's baton was provided to 16 healthy subjects, divided into 2 different groups depending on the years of musical training they had received (musicians or non-musicians). Ad hoc-created melodies, including notes of different durations, were played to the subjects. Each subject was asked to move the baton up and down according to the changes in pitch contour. Software for video analysis and modelling (Tracker®) was used to track the movement of the baton tip. The main parameters used for the analysis were the velocity peaks in the vertical axis. In the musician group, the number of velocity peaks exactly matched the number of notes, while in the non-musician group, the number of velocity peaks exceeded the number of notes. An exploratory data analysis using Poincaré plots suggested a greater degree of coupling between hand-arm movements and melody in musicians both with isochronous and non-isochronous rhythms. The calculated root mean square error (RMSE) between the note onset times and the velocity peaks, and the analysis of the distribution of velocity peaks in relationship to note onset times confirmed the effect of musical training. Notwithstanding the small number of participants, these results suggest that this novel behavioural task could be used to investigate auditory-motor coupling in the context of music in an ecologically valid setting. Furthermore, the task may be used for rhythm training and rehabilitation in neurological patients with movement disorders.