The aim of this study was to describe clinical, structural and biochemical factors associated with knee pain in younger subjects. A cross-sectional convenience sample of 371 male and female subjects (mean age, 45 years, range 26-61) was studied. Knee pain was assessed by questionnaire. Chondral defects, cartilage volume, and bone area of the right knee were determined using T1-weighted fat saturation magnetic resonance imaging (MRI). X-ray was performed on the same knee for the assessment of radiographic features of osteoarthritis. The urinary C-terminal cross-linking telopeptide of type II collagen (CTX-II) was measured by enzyme-linked immunosorbent assay (ELISA). Height and weight were measured by standard protocols and body mass index (BMI) was calculated. The prevalence of knee pain was 35% in this sample. Chondral defect scores (particularly femoral and patellar but not tibial) were significantly associated with knee pain in a dose-response fashion (all p<0.01). Cartilage volume and bone area were not associated with knee pain in multivariate analysis in this sample. Urinary CTX-II was higher in subjects with knee pain (p=0.04), but this became nonsignificant after adjustment for BMI and osteophytes (both of which were significant) suggesting potential mechanisms of effect. In conclusion, knee pain is significantly associated with non-full thickness chondral defects (particularly femoral and patellar), osteophytes, CTX-II, and obesity but not other factors. MRI and biochemical measures can add to radiographs in defining unexplained knee pain in younger subjects.