Our aim was to find an optimal method for monitoring disease progression and assessing the effectiveness of new agents in SOD1 mice. We compared six testing methods including clinical grading, weighing, hanging wire test, rotarod test, motor neuron counting and motor unit number estimation (MUNE) in SOD1 mice and control animals. The six methods were all able to differentiate between control animals and SOD1 transgenic mice at some time points; of them motor neuron counting, weighing and MUNE could detect abnormalities in presymptomatic stage in SOD1 mice; The number of functional motor units precisely correlated with motor neuron counts (r = 0.894, p<0.01). We concluded that MUNE is the better testing measure for monitoring disease and evaluating pharmacological therapies in SOD1 mice, which not only can reflect a meaningful biological effect of the agents used, but also is a sensitive, accurate and practical method.