Since secondary metabolites are involved in fungal-host interactions, those of endophytes and their hosts were studied to try to understand why endophytic infections remain symptomless. A screening of fungal isolates for biologically active secondary metabolites (antibacterial, antifungal, herbicidal) showed that the proportion of endophytic isolates that produced herbicidally active substances was three times that of the soil isolates and twice that of the phytopathogenic fungi. As markers for the plant defence reaction, the concentrations of certain phenolic metabolites were chosen. Those that differed in concentration were higher in the roots of plants infected with an endophyte than in those infected with a pathogen. The results presented here were regarded together with previous studies on other aspects of the plant defence response using dual cultures of plant host calli and endophytes, and of cell suspension cultures following endophytic as compared to pathogenic elicitation. The following hypothesis was developed: both the pathogen-host and the endophyte-host interactions involve constant mutual antagonisms at least in part based on the secondary metabolites the partners produce. Whereas the pathogen-host interaction is imbalanced and results in disease, that of the endophyte and its host is a balanced antagonism.