Objective To evaluate the reliability of the motor function measure (MFM) scale in the assessment of disease severity and progression when administered at home and clinic and assess its correlation with the Paediatric Outcomes Data Collection Instrument (PODCI). Methods In this prospective study, two assessors rated children with hereditary neuromuscular diseases (HNMDs) using the MFM at the clinic and then 2 weeks later at the patients' home. Intraclass correlation coefficient (ICC) was calculated for the reliability of the MFM and its domains. The reliability of each item was assessed and the correlation between MFM and three domains of PODCI was evaluated. Results A total of 48 children (5-17 years of age) were assessed in both locations and the MFM scale demonstrated excellent inter-rater reliability (ICC, 0.98). Weighted kappa ranged from excellent to poor. Correlation of the home-based MFM with the PODCI domain 'basic mobility and transfers' was excellent, with the 'upper extremity' domain was moderate, but there was no correlation with the 'happiness' domain. Conclusion The MFM is a reliable tool for assessing patients with HNMD when used in a home-based setting.