Background. Low back pain (LBP) and neck pain (NP) are common conditions in old age, leading to impaired functional ability and decreased independence. Manual and exercise therapies are common and effective therapies for the general LBP and NP populations. However, these treatments have not been adequately researched in older LBP and NP sufferers. The primary aim of these studies is to assess the relative clinical effectiveness of 1) manual treatment plus home exercise, 2) supervised rehabilitative exercise plus home exercise, and 3) home exercise alone, in terms of patient-rated pain, for senior LBP and NP patients. Secondary aims are to compare the three treatment approaches in regards to patient-rated disability, general health status, satisfaction, improvement and medication use, as well as objective outcomes of spinal motion, trunk strength and endurance, and functional ability. Cost-effectiveness and cost-utility will also be assessed. Finally, using qualitative methods, older LBP and NP patient's perceptions of treatment will be explored and described. Methods/Design. This paper describes the design of two multi-methods clinical studies focusing on elderly patients with non-acute LBP and NP. Each study includes a randomized clinical trial (RCT), a cost-effectiveness study alongside the RCT, and a qualitative study. Four hundred and eighty participants (240 per study), ages 65 and older, will be recruited and randomized to one of three, 12-week treatment programs. Patient-rated outcome measures are collected via self-report questionnaires at baseline and at 4, 12, 26, and 52 weeks post-randomization. Objective outcomes are assessed by examiners masked to treatment assignment at baseline and 12 weeks. Health care cost data is collected through standardized clinician forms, monthly phone interviews, and self-report questionnaires throughout the study. Qualitative interviews using a semi-structured format are conducted at the end of the 12 week treatment period. Discussion. To our knowledge, these are the first randomized clinical trials to comprehensively address clinical effectiveness, cost-effectiveness, and patients' perceptions of commonly used treatments for elderly LBP and NP sufferers. Trial Registration. NCT00269321 and NCT00269308.