Twenty-five fungal isolates were isolated from the collected soil samples from contaminated area, of Ain Helwan, Cairo, Egypt. All isolates were capable of growing on media containing 1.0 g/L of Nickel, Lead or Cobalt. The most potent fungal isolates that tolerate high heavy metal concentrations were morphologically identified as Penicillium sp., Asperagillus niger. and Rhizopus sp. These fungal isolates have recorded high tolerance index toward the tested heavy metals. Dispersive X-ray microanalysis (SEM-EDX) was used for the detection of the fate of metals present in fungal cells (before and after heavy metal treatment). The obtained data as a result of Dispersive X-ray microanalysis (SEM-EDX) application revealed the presence of high concentrations of the experimental heavy metal ions (Pb2+, Ni2+ and Co2+) in the isolated fungal cells. Also, their replacement of Ca++ ions in some cases and the detection of monovalent ions interruption such as K+ and Na+, in the cell of the treated fungal isolate.