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<i>Clostridium perfringens</i> toxinotype D, toxinotype E, and gastroenteritis-linked BEC/CPILE-positive strains have never been reported in healthy children. We isolated, whole-genome sequenced and bioinformatically characterised three <i>C. perfringens</i> isolates&#8212;type D (IQ1), type E (IQ2) and BEC/CPILE-positive (IQ3), recovered from the stools of three healthy two-year-olds, which were further compared to 128 <i>C. perfringens</i> genomes available from NCBI. The analysis uncovered a previously under-described putative toxin gene <i>alv</i> (alveolysin) encoded by isolates IQ2 and IQ3, which appeared to be a clade-specific trait associated with strains from domestic animals. A plasmid analysis indicated that the iota-toxin was encoded on a near-intact previously described plasmid pCPPB-1 in type E strain IQ2. The BEC genes <i>becA</i> and <i>becB</i> were carried on a near-identical pCPOS-1 plasmid previously associated with Japanese gastroenteritis outbreaks. Furthermore, a close phylogenetic relatedness was inferred between the French <i>C. perfringens</i> type E isolates cp515.17 and newly sequenced IQ2, suggesting geographical links. This study describes novel <i>C. perfringens</i> isolates from healthy individuals which encode important toxin genes, indicating the potential spread of these veterinary and clinically important strains and mobile genetic elements, and highlights areas for future research.