Embryo quality assessment by optical imaging is increasing in popularity. Among available optical techniques, light sheet microscopy has emerged as a superior alternative to confocal microscopy due to its geometry, enabling faster image acquisition with reduced photodamage to the sample. However, previous assessments of photodamage induced by imaging, may have failed to measure more subtle impacts. In this study, we employed DNA damage as a sensitive indicator of light induced damage. We use light sheet microscopy with excitation at a wavelength of 405 nm for imaging embryo autofluorescence and compare its performance to laser scanning confocal microscopy at the same wavelength. At an equivalent signal-to-noise ratio for images acquired with both modalities, light sheet microscopy reduces image acquisition time by 10-fold. Further, light sheet microscopy at this excitation wavelength does not induce DNA damage when compared to non-imaged embryos. In contrast, imaging with confocal microscopy led to significantly higher levels of DNA damage within embryos. This study confirms that light sheet microscopy is faster and safer than confocal microscopy for imaging embryos, indicating its potential as a label-free diagnostic for embryo quality.