The aetiology of diarrhoea with Cryptosporidium species and pathogenic bacteria has not been identified in the Ethiopian primary healthcare system. Thus, antibiotic consumption for unconfirmed pathogenic diarrhoea is not infrequent. A total of 344 children aged <5 years with diarrhoea were included in the present study to determine protozoal or bacterial aetiology and antibiotic use. Overall, 47.1% of children with diarrhoea had either protozoan or bacterial pathogens. The prevalence of Cryptosporidium species was 12.8% while bacterial pathogens were 13.1%. Based on direct microscopic stool examination, 77.6% (267/344) of children with diarrhoea were treated with antimicrobials. Of these, 16.7%–51.4% of prescribed antimicrobials were appropriate. None of the children with Cryptosporidium diarrhoea were treated with the appropriate antimicrobial. Enteric bacterial pathogens showed a resistance of 51.6% to cotrimoxazole. Empirical treatments are not appropriate for the majority of child cases of diarrhoea.
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