Colour alteration indices (CAIs) of conodonts in Peninsular Malaysia range in value from 1.5 to 8. The lowestvalues are found in Triassic Limestones in northwest Peninsular Malaysia and the highest values occur in Palaeozoicstrata within or close to zones of deformation or to intrusives. Palaeozoic conodonts from the SibumasuBlock (Western Belt of Peninsular Malaysia) show how a background value of CAI 5; all conodonts of Ordovicianto Middle Permian age have CAIs of at least 5 and locally up to 8. Palaeozoic conodonts of Sibumasu exhibittextural alteration interpreted as the result of regional metamorphism, whereas Triassic conodonts exhibit littletextural alteration. The disparity between CAIs and textural alteration of Palaeozoic vs Triassic conodonts ofSibumasu suggests regional metamorphism of these rocks around the Palaozoic-Mesozoic boundary, whichis consistent with the previously suggested time for the initial collision between the Sibumasu and Indochinablocks. Upper Palaeozoic conodonts from the Indochina Block (Central and Eastern Belts), however, are morevariable. Upper Lower Carboniferous (Namurian) conodonts from the Panching Limestone in the Eastern Beltexhibit a CAI of 3 and appear to have escaped the effects of the regional metamorphism that affected the coevalrocks on the Sibumasu Block. Permian conodonts from limestones along the western margin of the Central Belthave an anomalously high CAI of 5, probably caused by the healing effect of the Main Range granitoids.