Purpose: To investigate, in patients after stroke with a very weak upper limb, the profile of recovery for upper limb activity over the first 12 weeks, and whether early secondary impairments predict later upper limb activity. Method: Forty patients within 2 weeks of stroke with a very weak upper limb (<4/6 Item 6 of Motor Assessment Scale) were observed longitudinally. Upper limb activity (Items 6, 7, and 8 of Motor Assessment Scale), shoulder subluxation (vertical distance), shoulder pain (visual analogue scale), and upper limb range of motion were measured at 2, 6, and 12 weeks poststroke. Results: By Week 12, upper limb activity was 1.0/18 (IQR 3.0). Shoulder subluxation was 42 mm (SD 8), 7 mm > the intact side at 2 weeks. Pain at rest was 0.1/10 (IQR 1.1), and pain during movement was 2.6/10 (IQR 4.5). Passive shoulder external rotation was 23° (SD 34), 30% of the intact side at 2 weeks. Shoulder pain during movement at 2 weeks predicted shoulder pain during movement at 6 and 12 weeks after stroke (p = 0.05). Conclusion: Most patients with a disabled upper limb after stroke have little recovery of activity in the first 12 weeks. Shoulder pain on movement at 2 weeks should be flagged as a predictor of future pain.