The objective of this preliminary study was to examine the possible contribution of disordered control of motor unit (MU) recruitment and firing patterns in muscle weakness post-stroke. A novel surface EMG (sEMG) recording and decomposition system was used to record sEMG signals and extract single MU activities from the first dorsal interosseous muscle (FDI) of two hemiparetic stroke survivors. To characterize MU reorganization, an estimate of the motor unit action potential (MUAP) amplitude was derived using spike triggered averaging of the sEMG signal. The MUs suitable for further analysis were selected using a set of statistical tests that assessed the variability of the morphological characteristics of the MUAPs. Our preliminary results suggest a disrupted orderly recruitment based on MUAP size, a compressed recruitment range, and reduced firing rates evident in the paretic muscle compared with the contralateral muscle of one subject with moderate impairment. In contrast, the MU organization was largely similar bilaterally for the subject with minor impairment. The preliminary results suggest that MU organizational changes with respect to recruitment and rate modulation can contribute to muscle weakness post-stroke. The contrasting results of the two subjects indicate that the degree of MU reorganization may be associated with the degree of the functional impairment, which reveals the differential diagnostic capability of the sEMG decomposition system.