The aim of this investigation is to assess effect of three different bleaching techniques on structural integrity, mineral density and volume of enamel via micro-computed tomography (micro-CT) and examine color changes by CIELAB and CIEDE2000 formulas. Twenty-four upper premolar teeth were randomly separated into three different groups (n = 8) (group 1, 35% hydrogen peroxide (HP) gel with Er,Cr:YSGG laser activation; group 2, 35% HP gel with diode laser activation; group 3, 35% HP gel with chemically activation). High-resolution micro-CT system (Bruker Skyscan 1275, Kontich, Belgium) was carried out to scan samples. Each tooth was scanned twice before-after application of bleaching with same scanning parameters. Structural thickness, structural separation, fragmentation index, mineral density, and mineral volume of enamel were calculated for each region of interest (ROI). Color changes were measured with spectrophotometer and calculated with CIELAB and CIEDE2000 formulas. Data analysis was made with one-way ANOVA with post-hoc LSD. Micro-CT analysis indicated that statistically significant differences were found in structural thickness, and separation, mineral density, and mineral volume of enamel for different ROIs before and after whitening for whole groups (P < .05). Significant differences were detected among inter-groups for these parameters in different ROIs (P < .05). There was no significant difference among groups for color alterations (P > .05). All bleaching applications exhibited similar efficiency on the enamel surface. Nevertheless, bleaching process with Er,Cr:YSGG laser had less negative effects on enamel as it showed less change in enamel compared to other bleaching treatments. Micro-CT analysis of histomorphometric parameters can be useful for further mineralization studies of dental hard tissues.