Cariogenic bacterial acids dissolve the inorganic elements in dentine, leaving the dentine matrix exposed. Host-derived matrix metalloproteinases (MMPs) play an essential role in caries progression as they are significant regulators of extracellular matrix turnover and can degrade exposed collagen. This paper investigates the expression of MMP2 and MMP9 across various stages of caries in primary human teeth and relate this with a diagnosis recorded by the International Caries Detection and Assessment System (ICDAS). Twenty-four sections (150 μm in thickness) from extracted teeth, clinically diagnosed using ICDAS, were immunohistochemically treated with monoclonal anti-MMP2 and anti-MMP9 antibodies. Positive staining was visualised by immunofluorescence using a VectorFluor Duet Double Labeling Kit. Images from triplicate samples for each ICDAS score were analysed using ImageJ software. Collagen degradation in caries lesions was detected using a hydroxyproline assay. MMPs were weakly detected in caries with ICDAS 1-2 scores, and an insignificant increase was detected in ICDAS 3. However, a significant increase in MMP expression was seen in caries with an ICDAS score of 4-6. There was a strong positive correlation between the ICDAS score and MMP2 (r [6] = 0.86, p = 0.002) and between ICDAS and MMP9 (r [6] = 0.82, p = 0.004). Data were analysed using two-way ANOVA followed by Tukey multiple comparison test (*p < 0.05). The use of ICDAS to assess the severity of caries lesions and how this correlates with the presence of MMP in these lesions validates the modern approach to caries management with a minimally invasive concept.