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According to the degree of upper and lower motor neuron degeneration, motor neuron diseases (MND) can be categorized into amyotrophic lateral sclerosis (ALS), primary lateral sclerosis (PLS) or progressive muscular atrophy (PMA). Although several studies have addressed the prevalence and incidence of ALS, there is a high heterogeneity in their results. Besides this, neither concept has been previously studied in PLS or PMA. Thus, the objective of this study was to estimate the prevalence and incidence of MND, (distinguishing ALS, PLS and PMA), in the Spanish regions of Catalonia and Valencia in the period 2011-2019. Two population-based Spanish cohorts were used, one from Catalonia and the other from Valencia. Given that the samples that comprised both cohorts were not random, i.e., leading to a selection bias, we used a two-part model in which both the individual and contextual observed and unobserved confounding variables are controlled for, along with the spatial and temporal dependence. The prevalence of MND was estimated to be between 3.990 and 6.334 per 100,000 inhabitants (ALS between 3.248 and 5.120; PMA between 0.065 and 0.634; and PLS between 0.046 and 1.896), and the incidence between 1.682 and 2.165 per 100,000 person-years for MND (ALS between 1.351 and 1.754; PMA between 0.225 and 0.628; and PLS between 0.409-0.544). Results were similar in the two regions and did not differ from those previously reported for ALS, suggesting that the proposed method is robust and that neither region presents differential risk or protective factors.