Abstract Post-mortem examination of embryos and fetuses becomes increasingly important due to the development of prenatal diagnostic methods. Possibilities of visualization of embryonic and fetal heart in echocardiography and autopsy develops rapidly and due to learning curve there is a need for confirmation of results. There are different methods for visualization of cardiac anatomy. Some morphologists prefer classical histology while others use stereomicroscopy. Objectives: To develop our own autopsy routine for embryonic and small fetal hearts. Material and methods: Twenty five normal and malformed fetal hearts aged from 7 to 12 weeks, fixed and unfixed, were submerged in saline solution and dissected using microsurgical instruments. Nikon SMZ 1500 microscope, Nikon DS-Fi1 camera and NIS-Elements 3.00 software were used for observation and documentation. The chest was opened by median sternotomy, the heart was dissected in situ and sequential segmental analysis was applied. Results: Detailed anatomy of atriums, interatrial septum, pulmonary and systemic veins drainage were examined. In all cases it was possible to assess morphology of chambers, atrioventricular and ventriculoarterial connections. Congenital heart defect was diagnosed in only 3 out of 25 cases: one in the 10th week of gestation (complete atrioventricular septal defect – CAVSD) and two in the 12th week of gestation (1 case of CAVSD with trisomy 21 confirmed cytogenetically and one of tetralogy of Fallot). Conclusion: Microautopsy of fetal heart in the 1st trimester of pregnancy is possible using stereomicroscopy and allows us to diagnose congenital heart diseases. Detailed structures are best visible when specimen is unfixed and submerged in saline solution.