Purpose: Using atomic force microscopy (AFM), the purpose was to investigate the effect of phosphoric acid (H3PO4) concentration and etching duration on surface roughness (Ra) and micromorphology of enamel and dentin substrates of uremic patients receiving hemodialysis. Materials and Methods: Sixty-three enamel and dentin slabs were prepared from 42 sound natural molars collected from uremic patients under hemodialysis and mechanically polished up to 4000-grit roughness. Nine slabs of each substrate were not etched (control group). The remaining slabs were divided into two experimental groups (n = 27) according to etchant concentration (37% or 42%). In each group, 9 specimens were etched for 15, 30, and 60 s. The surface morphology of the control and test specimens was examined by AFM operated in "contact" mode. The obtained Ra was subjected to statistical analysis. Results: Statistical analysis showed that increasing the duration of acid application (irrespective of acid concentration and type of substrate) significantly increased the amount of Ra. H3PO4 at a concentration of 42% was more effective at producing Ra than was H3PO4 at 37% for all 3 application times. The Ra quantity produced by H3PO4 at 42% was time specific, with 15 s being significantly less effective than 30 or 60 s. However, 60 s was significantly better than 30. Conclusion: The findings of this study support the use of 42% H3PO4 for etching uremic hard tooth tissues for 60 s. Keywords: uremia, etchant concentration, etching duration, enamel and dentin, surface roughness