Aspergillus niger is capable of removing heavy metals such as lead, cadmium and copper from aqueous solutions. The role played by various functional groups in the cell wall of A. niger in biosorption of lead, cadmium and copper was investigated. The biomass was subjected to chemical treatments to modify the functional groups, carboxyl, amino and phosphate, to study their role in biosorption of metal ions. The modifications of the functional groups which resulted from these chemical treatments were examined with infrared spectroscopy. It was found that esterification of carboxyl and methylation of amine groups present in the cell wall of A. niger significantly decreased biosorption of the heavy metals studied. These findings suggest that carboxylate and amine groups are important in metal ion biosorption on A. niger biomass. Phosphate groups and the lipids fraction of the biomass did not play a significant role in biosorption of the metal ions studied. Biosorption of lead and cadmium displaced Ca2+, Mg2+ and K+ ions present on the biomass surface, indicating that biosorption took place as a result of an ion-exchange process.