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The aim of this study was to evaluate the ability of visual examination (International Caries Detection and Assessment System—ICDAS II), light-emitting diodes (LED) fluorescence (SPECTRA), laser fluorescence (DIAGNODent, DD), photothermal radiometry and modulated luminescence (PTR-LUM, The Canary System, CS) to detect natural decay beneath resin-modified glass ionomer (RMGIC) and compomer restorations in vitro. Twenty-seven extracted human molars and premolars, consisting of 2 control teeth, 10 visually healthy/sound and 15 teeth with natural cavitated lesions, were selected. For the carious teeth, caries was removed leaving some carious tissue on one wall of the preparation. For the sound teeth, 3 mm deep cavity preparations were made. All cavities were restored with RMGIC or compomer restorative materials. Sixty-eight sites (4 sites on sound unrestored teeth, 21 sound sites and 43 carious sites with restorations) were selected. CS and DD triplicate measurements were done at 2, 1.5, 0.5, and 0 mm away from the margin of the restoration (MOR). SPECTRA images were taken, and two dentists provided ICDAS II scoring for the restored surfaces. The SPECTRA data and images were inconclusive due to signal interference from the restorations. Visual examinations of the restored tooth surfaces were able to identify 5 of the 15 teeth with caries. In these situations, the teeth were ranked as having ICDAS II 1 or 2 rankings, but they could not identify the location of the caries or depth of the lesion. CS and DD were able to differentiate between sound and carious tissue at the MOR, but larger variation in measurement, and poorer accuracy, was observed for DD. It was concluded that the CS has the potential to detect secondary caries around RMGIC and compomer restorations more accurately than the other modalities used in this study.