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This retrospective study described the aetiologies of neonatal diarrhoea cases and their associations with histological findings. A total of 106 diarrhoeic neonatal piglets were selected. Cultures, MALDI typings, PCRs and evaluation of intestinal lesions were performed. A total of 51 cases (48.1%) were positive for only one pathogen and 54 (50.9%) were positive for more than one pathogen. <i>Clostridium perfringens</i> type A was the most frequently detected pathogen (61.3%), followed by <i>Enterococcus hirae</i> (43.4%), rotavirus type A (38.7%), rotavirus type C (11.3%) and enterotoxigenic <i>Escherichia coli</i> (3.8%). Only lesions in the small intestine were correlated with detected pathogens. The detection of rotavirus was associated with an increased probability of observing villous atrophy (<i>p</i> < 0.001), crypt hyperplasia (<i>p</i> = 0.01) and leucocyte necrosis in the lamina propria (<i>p</i> = 0.05). The detection of <i>Clostridium perfringens</i> type A was associated with an increased probability of observing bacilli in close proximity to the mucosa (<i>p</i> < 0.001) and a decreased probability of observing epithelial necrosis (<i>p</i> = 0.04). Detection of <i>Enterococcus hirae</i> was associated with an increased probability of observing enteroadherent cocci (<i>p</i> < 0.001). Multivariate regression logistic models revealed that epithelial necrosis was more likely to occur in <i>Enterococcus hirae</i>-positive piglets (<i>p</i> < 0.02) and neutrophilic infiltrate was more likely to occur in <i>Clostridium perfringens</i> type A- and <i>Enterococcus hirae</i>-positive piglets (<i>p</i> = 0.04 and <i>p</i> = 0.02, respectively).