Magnetic resonance imaging (MRI) and computed tomography (CT) are noninvasive medical imaging techniques used for the detailed visualization of internal organs of the human body.Because CT uses X-rays for imaging, there is a risk of radiation exposure.In contrast, MRI uses radiowaves and magnetic fields for imaging; thus, there are no reported biological hazards.However, neither MRI nor CT is suitable as a noninvasive imaging tool applicable in small laboratory animals such as zebrafish embryos or larvae.The recently established micro-CT scanner is only suitable for scanning adult fish and a staining procedure is required for imaging.In addition, CT-based scanning is generally more suitable for skeletal imaging but not for visualization of soft tissues because of its lower contrast.In this study, we evaluated whether 633nm HeNe laser-coupled confocal microscope allows simulating MRI/CT scan and imaging soft tissues such as brain and eye in zebrafish embryos/larvae.We show that the 633nm HeNe laser can penetrate well into intact brain and eye of zebrafish.It represents a noninvasive imaging method with high resolution while not requiting contrast agents, enabling the detection of differential signals from normal and pathological organs such as brain and eye.