Hereditary spastic paraplegias (HSP) represents a group of orphan neurodegenerative diseases with gait disturbance as the predominant clinical feature. Due to its rarity, research within this field is still limited. Aside from clinical analysis using established scales, gait analysis has been employed to enhance the understanding of the mechanisms behind the disease. However, state of the art gait analysis systems are often large, immobile and expensive. To overcome these limitations, this paper presents the first clinically relevant mobile gait analysis system for HSP patients. We propose an unsupervised model based on local cyclicity estimation and hierarchical hidden Markov models (LCE-hHMM). The system provides stride time, swing time, stance time, swing duration and cadence. These parameters are validated against a GAITRite system and manual sensor data labelling using a total of 24 patients within 2 separate studies. The proposed system achieves a stride time error of -0.00 ± 0.09 s (correlation coefficient, r = 1.00) and a swing duration error of -0.67 ± 3.27 % (correlation coefficient, r = 0.93) with respect to the GAITRite system. We show that these parameters are also correlated to the clinical spastic paraplegia rating scale (SPRS) in a similar manner to other state of the art gait analysis systems, as well as to supervised and general versions of the proposed model. Finally, we show a proof of concept for this system to be used to analyse alterations in the gait of individual patients. Thus, with further clinical studies, due to its automated approach and mobility, this system could be used to determine treatment effects in future clinical trials.