In Denmark, lesions indicating acute generalised infection identified at meat inspection will result in total condemnation. An official bacteriological examination (BU) protocol can be used for slaughtered animals with lesions such as endocarditis and endophlebitis as an assisting diagnostic tool to confirm whether the condition is local or generalised. If local, the carcass can be approved after condemnation of the relevant organs. The BU involves cultivating samples from the spleen and muscle. The aim of this study was to assess the value of the BU protocol. The study was conducted from February to May 2019 at a Danish cattle abattoir. Three groups of slaughtered cattle were included: 24 cases consisting of cattle with endocarditis and endophlebitis, 25 control animals consisting of cattle fully approved at inspection and 16 animals condemned at inspection due to endocarditis and endophlebitis with complications. Samples were taken from the heart, liver, kidney, lung, spleen and muscles of each animal. The BU protocol was used for cultivation. Different types of colonies were identified using MALDI-TOF-MS analysis. One or more samples with bacterial growth were found in all condemned animals – in 16 out of the 24 case animals and in two out of 25 control animals. In all three groups, Trueperella pyogenes was the most frequently isolated bacterium (60%) followed by Fusobacterium necrophorum (10%). For the case animals, the organ most commonly found with bacterial growth was the liver (46%), followed by the lung (38%) and the kidney (38%), while 96% of the muscle samples were negative. For the condemned group, bacterial growth was found in 75% of the spleen samples, 56% of liver and lung samples, and 50% of the muscle samples. A statistical analysis of the samples from cases and controls showed strong pair-wise associations for the presence of bacteria between organs, but no pair-wise associations between presence of bacteria in the muscle and any of the organs. Hence, if bacteria are found e.g. in the liver, they are likely to be found in other organs, but not in the muscle. In total, 20 of the 24 case animals were fully or partly approved in accordance with the current rules for judgement. It was concluded that the BU protocol using spleen and muscle samples would be suitable as a diagnostic tool for the judgement of slaughtered animals in cases where there is doubt about the stage of the lesions observed.