The characteristics and variability of the short latency responses to transcranial magnetic stimulation (TMS) were examined in 188 single lower limb motor units. Information about the cortically evoked postsynaptic potentials was derived from peristimulus time histograms generated from the discharge times of single, rhythmically active, motor units. Tibialis anterior (TA) motoneurons were almost exclusively facilitated and response magnitudes were consistent within a motoneuron pool as indicated by low coefficients of variation (CV). The net cortical effect on soleus (SOL) and medial gastrocnemius (MG) motoneurons was significantly weaker than in TA (P < 0.001) and the responses were non-homogeneous within a motoneuron pool, both in terms of response amplitude and direction. The occurrence of strong facilitatory and inhibitory responses or an absence of a response within a given MG motoneuron pool was associated with CVs about 13 times that of TA and 4 times that of SOL. The large CVs may be indicative of the existence of subgroups of motoneurons differentiated by their response to TMS. Examination of only excitatory responses resulted in comparable CVs across the muscles tested. It is suggested that the degree of non-homogeneity within a motoneuron pool reflects the ability of the cortex to modulate other inputs. Selective cortical activation of specific groups (or subgroups) of motoneurons may set up appropriate conditions suited to a particular volitional task.