Small supernumerary marker chromosomes (sSMC) in human are present in 0.043% of newborn children. They can be defined as additional centric chromosome fragments smaller than chromosome 20. sSMC include cases with the i(18p)-, the i(12p)- (i.e. Pallister Killian-) or the inv dup(22)- (i.e. cat-eye-) syndrome. However, about 30% of the remaining sSMC are not yet correlated with clinical syndromes, mostly due to problems in comprehensive characterisation of the sSMC. Here we present an overview of the approaches for sSMC characterisation and suggest a strategy for a straightforward and comprehensive characterisation of the marker chromosomes in question.