Severity of root-rot and stalk-rot of maize and soybean plants as well maize late wilt diseases were higher under intercropping than sole cropping conditions. The percentage of infection and disease severity of soybean and maize plants as well as precentage of maize late wilt were high in some districts of El-Sharkia Governorate. It could be concluded that microbial-flora are increased in the rhizosphere of maize and soyb­ean under intercropping compared with sole cropping conditions. The higher microbial densities could be easily observed 75 days after sowing under intercropping system. Root exudates of maize and soybean plants under both sole and intercropping increased the growth of the pathogenic, fungal dry weight. Root exudates of soybean and maize plants under intercropping condi­tions increased dry weight of the pathogenic fungi compared with root exudates of both plants under sole cropping system. Root exudates of maize plants had four amino acids, while soybean root exudates had eleven amino acids. The root exudates of maize and soybean under in­tercropping system had eleven amino acids. Maize root exudates had a higher content of sugars compared with soybean root exudates.