Small supernumerary marker chromosomes (SMCs) in human can be defined as additional centric chromosome fragments smaller than chromosome 20. For most small or minute SMCs a correlation with clinical symptoms is lacking, mostly due to problems in visualizing their euchromatic content. Recently we described two new molecular cytogenetic approaches for the comprehensive characterization of small SMCs, excluding those few cases with neo-centromeres. Minute SMCs, consisting preferentially of alpha-satellite DNA, are characterizable in one step by the centromere-specific multicolor FISH (cenM-FISH) approach. For further characterization of minute SMCs and eventually present euchromatic content, the recently developed centromere-near-specific multicolor FISH (subcenM-FISH) technique can be applied. These two approaches are highly informative and easy to perform, as demonstrated in the present report on the example of a prenatal case with a minute SMC derived from chromosome 3 cytogenetically described as min(3)(:p12.1 --> q11.2:).