More accurate and sensitive visualisation of faecal contamination in the abattoir would significantly reduce the risk posed by harbouring pathogenic micro-organisms. We carried out a preliminary investigation of the range of fluorophores found naturally in faeces from typical ruminant diets. Sixteen ewes were offered either: i) fresh forage (FF), ii) grass silage (GS), iii) grass hay (GH) or iv) concentrate and barley straw (CB). Animals offered FF diets had a greater concentration (P <0.001) of chlorophyll based compounds in their faeces and subsequent fluorescent emission spectra. In a second experiment we investigated a range of fluorescent markers against a basal concentrate and barley straw diet. Ten Cheviot sheep were split into five treatment groups during a duplicate 5 × 5 Latin square design. Four of the groups received a chlorophyll based marker at a rate of 2 g/d: i) Mg–Chlorophyllin (MgC), ii) Fe–Chlorophyllin (FeC), iii) Zn–Chlorophyllin (ZnC) or iv) Spirulina (Chlorophyll a extract from blue green algae, Sp). The last group received no supplement as the control (Con). The appearance of chlorophyllin markers and their derivatives in faeces was similar with mean concentrations of 3.1 and 7.2 μg/g DM, respectively. The most intense fluorescent signal was shown with MgC followed by ZnC, FeC, Sp and Con at 685 nm. The use of markers in pre-slaughter diets would improve the accuracy of faecal detection as a result of greater fluorescence and specific emission wavelengths which do not overlap with natural meat components to help with visualisation.