Intervertebral disc degeneration has been widely studied in different animal models. To test the hypothesis that needle puncture could induce progressive biochemical and molecular changes in murine discs, we established a mouse tail model to investigate the pathogenesis and molecular mechanism of puncture-induced disc degeneration. Caudal discs in mouse tails were punctured using a 31G gauge needle at controlled depth under microscopic guidance. The progress of the disc degeneration was evaluated by radiographic analysis of disc height, histological grading and glycosaminoglycan (GAG) quantification pre-operation and 1, 2, 6 and 12 weeks post-puncture. Gene and protein expression of the extracellular matrix (ECM) was analysed by RT-PCR, in situ hybridization and immunohistochemistry. Histological study and disc height analysis revealed progressive degenerative changes in the punctured discs. Compared with the pre-operation control group, total GAG content decreased 40% (p < 0.05) and aggrecan (Acan), decorin (Dcn) and versican (Vcan; Cspg2) expression was down-regulated at 12 weeks post-puncture. A transient increase of Col2a1-expressing cells and elevation of collagen II protein in the nucleus pulposus (NP) was detected. Fibronectin (Fn1) expression was up-regulated 50% and deposition of collagen I in NP was observed at 12 weeks post-puncture. This study is the first to use an injury-induced model to study disc degeneration in mouse. The disc degeneration involves a transient transformation of NP from notochordal to chondrogenic and eventually into fibrocartilaginous phenotype. The degenerative changes have some similarity to human disc degeneration, suggesting that this model may potentially be used in future to study the molecular mechanism and dissect the pathways of disc degeneration.