Little is known about potential long-term effects of body acupuncture. The aim of the study was to determine such long-term effects 3 and 6 months after the end of a course of acupuncture treatment for chronic low-back pain (cLBP) or chronic pain caused by gonarthrosis. Prospective cohort study with patients who had received 10 sessions of needle body acupuncture within a maximum of 10 weeks. Data source was our survey of all patients receiving acupuncture treatment in Germany. A total of 1096 eligible patients with cLBP or gonarthrosis pain were identified (68.1% female) and invited by letter to participate in the study. Ultimately 249 patients remained, with no loss of representativeness. Two telephone interviews were conducted 3 and 6 months after the last acupuncture session using standardized questionnaires, available as electronic case report forms. The primary target criteria were self-assessment of pain tolerability prior to the start of acupuncture and after the end of treatment, and pain intensity (GCPS) over time. Secondary target criteria were changes to functional impairment (HFAQ for cLBP, WOMAC for gonarthrosis), quality of life (SF12), depression (CES-D) and patient global assessment of treatment effectiveness (PGA). For the indication cLBP, pain-related fear avoidance beliefs (FABQ) were also queried. Pain tolerability before acupuncture was reported as being significantly worse than pain tolerability at the time of the two post-acupuncture interviews. The scores for all post-acupuncture questionnaires showed no significant changes over time, with the exception of treatment effectiveness for gonarthrosis. Mean scores for each of the questionnaires at the 3 and 6 month follow-up interviews were as follows: cLBP: Pain tolerability (pre: 6.8, post: 3.4 / 3.4), pain intensity (41.8 / 42.6), PGA (2.4 / 2.6), SF12 physical (35.8 / 35.8), SF12 mental (45.3 / 46.9), CES-D (14.9 / 14.9), HFAQ (67.2 / 67.1), FABQ total (2.9 / 2.9). GONARTHROSIS: Pain tolerability (pre: 6.9, post: 3.6 / 3.9), pain intensity (42.9 / 42.8), PGA (2.6 / 2.9), SF12 physical (32.2 / 31.3), SF12 mental (45.0 / 46.2), CES-D (15.6 / 14.7), WOMAC total (34.6 / 34.0). Pain tolerability was significantly improved after acupuncture and remained so up to 6 months after treatment. The mean scores of almost all questionnaires did not change significantly between 3 and 6 months. We therefore conclude that acupuncture had a long-term effect on important aspects of cognitive and emotional pain coping.