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Glenohumeral subluxation (GHS) is a frequent complication in patients with post-stroke hemiplegia, but its role in functional recovery is still unclear. The aim of the present investigation was to understand the relationship of GHS with shoulder pain and arm motor recovery.A case-control study design was used. A sample of 107 hemiplegic adults with recent stroke (less than 30 days from onset) was differentiated into two groups according to the presence of GHS. Motor recovery was assessed using the upper extremity part of the Fugl-Meyer Assessment Scale and the presence of shoulder pain was recorded at admission (T1), at discharge (T2) and at follow-up, 30–40 days after discharge (T3).GHS was present in 52 patients (48.6%) and correlated significantly to shoulder pain at T1, at T2 and at T3 (p < 0.001). Moreover, GHS at admission accounted for nearly 50% of shoulder pain at T3 (adjusted R2 = 0.458; p < 0.001). The presence of GHS was independently associated with the upper extremity score of the Fugl-Meyer Assessment Scale at follow-up (adjusted R2 = 0.766; p < 0.001).GHS is a factor associated with shoulder pain development and with arm motor recovery and should be treated in the acute stage of hemiplegia.