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This study aimed to research the involvement of enterotoxigenic <i>E. coli</i> (ETEC) and <i>C. difficile</i> or <i>C. perfringens</i> type C in the aetiology of neonatal piglet diarrhoea in Greece and to identify preventive factors for them. A total of 78 pooled faecal samples were collected randomly from 234 suckling piglets (1–4 days of age) with diarrhoea from 26 pig farms (3 piglets × 3 litters × 26 farms = 234 piglets = 78 faecal pool samples). The collected samples were initially screened for the presence of <i>E. coli</i> and <i>C. difficile</i> or <i>C. perfringens</i> via cultivation on MacConkey and anaerobic blood agar, respectively. Subsequently, the samples were pooled on ELUTE cards. From samples tested, 69.23% of those in the farms were ETEC F4-positive, 30.77% were ETEC F5-positive, 61.54% ETEC were F6-positive, 42.31% were ETEC F4- and <i>E. coli</i> enterotoxin LT-positive, 19.23% were ETEC F5- and LT-positive, 42.31% were ETEC F6- and LT-positive, while LT was found in 57.69% of those in the farms. <i>C. difficile</i> was involved in many cases and identified as an emerging neonatal diarrhoea etiological agent. Specifically, Toxin A of <i>C. difficile</i> was found in 84.62% and Toxin B in 88.46% of those in the farms. Antibiotic administration to sows in combination with probiotics or acidifiers was revealed to reduce the detection of antigens of ETEC and the enterotoxin LT of <i>E. coli</i>.