Background One of the primary difficulties in evaluating the effectiveness of lumbar fusion is that, with the exception of spondylolisthesis, specific diagnostic indications for surgery are poorly defined. Diagnostic specificity beyond the symptom of low back pain or the presence of lumbar degeneration needs to be delineated such that outcomes data can be effectively translated into clinical decision making or evidence-based guidelines. Purpose The purpose of this study was to report on prospectively collected clinical outcome measures, stratified by diagnosis, among a series of patients with lumbar degenerative disease whose treatment included lumbar spine fusion. Study design Demographics, diagnostic categorization, and clinical outcome measures were prospectively collected by six spine surgeons at a single tertiary spine center, as part of the surgeons' standard clinical practice. Patient sample Four hundred and twenty-eight patients were enrolled in the study and complete 1- and 2-year Health-Related Quality of Life (HRQOL) data were available in 327 patients whose treatment included decompression and posterolateral lumbar fusion. Outcome measures The Oswestry Disability Index (ODI), Short Form-36 (SF-36), numeric rating scales for back pain and leg pain. Methods Preoperative diagnosis was classified, in the primary surgical cases, as disc pathology, spondylolisthesis, instability, stenosis, or scoliosis. In revision cases, the diagnosis was classified as nonunion, adjacent level degeneration, or postdiscectomy revision. Patient-reported outcomes at 1 and 2 years post-op were assessed based on diagnostic stratification. Statistical evaluation of clinical outcome was performed for both mean net change in outcome scores and the percentage of patients reaching a minimum clinically important difference (MCID) threshold for each outcome measure. Results Preoperative diagnosis was spondylolisthesis (n=80), scoliosis (n=17), disc pathology (n=33), instability (n=21), stenosis (n=46), postdiscectomy revision (n=67), adjacent level degeneration (n=40), or nonunion (n=23). Evaluation of 2-year post-op HRQOL measures by diagnostic subgroup revealed the most substantial improvement in ODI score for patients with spondylolisthesis (22.7 points) and scoliosis (21.2 points). Patients with the diagnosis of disc pathology (16.2 points), postdiscectomy revision (14.0 points), instability (12.7 points), stenosis (10.6 points), and adjacent level degeneration (9.5 points) demonstrated a progressively smaller magnitude of ODI improvement. The least ODI improvement at 2 years after surgery was seen in patients with nonunion of a prior fusion (5.5 points). The percentage of patients reaching MCID for ODI at 2 years post-op ranged from 71.0% in the spondylolisthesis subgroup to 34.8% in the nonunion subgroup. The greatest SF-36 physical component score improvement at 2-year follow-up was seen in patients with disc pathology (7.9 points) and spondylolisthesis (7.7 points), followed by scoliosis (6.6 points) and stenosis (6.5 points), instability (5.6 points), postdiscectomy revision (5.3 points) nonunion (3.1 points) and adjacent level degeneration (2.5 points). No significant changes from Year 1 to Year 2 were noted in any of the subgroups. For SF-36 physical component score, percentage of patients reaching MCID ranged from 63.6% in the disc pathology subgroup to 25% in the nonunion subgroup. Conclusions This study supports the concept that added diagnostic specificity is a critical component in building an improved evidence base for lumbar fusion surgery. The magnitude of HRQOL improvement was not equal among diagnostic subgroups. The percentage of patients reaching an MCID level of improvement was also significantly influenced by diagnostic stratification. Without diagnostic specificity for entities beyond spondylolisthesis, the absence of well-defined study populations will continue to limit our ability to move toward evidence-based decision making.