Introduction: Chromosome abnormalities are an important cause of fetal and perinatal deaths. Molecular testing can be a useful tool in preconception counseling in selected families. However, such testing is neither routine nor mandatory at many healthcare centers; a number of factors can contribute to the lack of genetic and chromosome diagnoses. Materials and methods: We performed an observational analytical study on 42 paraffin-embedded samples from fetal autopsy tissue with the suspected chromosomal disorder; we tested the efficacy of the fluorescence in situ hybridization (FISH) probe to ascertain the presence of common chromosome abnormalities. Results: Use of the FISH technique in paraffin-embedded tissue has been standard practice in oncopathology; there now exists standardization of these probes in fetal and neonatal tissue. Our study analyzes various difficulties we encountered with the FISH probe when used for chromosome abnormalities diagnoses in fetal autopsies, and we conclude with pertinent recommendations for improving test outcomes. Conclusion: Simultaneous occurrence of chromosome disorders and advanced maceration is common; maceration interferes with the proper performance of the FISH test; however, we view this diagnostic tool as appropriately functional when used under specific conditions.