The hypotone neonate, floppy infant, often proves to be a diagnostic challenge, as the causes of floppy infant syndrome are many and often rare. In this case story a floppy girl was diagnosed with the rare, autosomal recessive disease pontocerebellar hypoplasia type I. The tests for the most common causes of floppy infant syndrome showed nothing abnormal, but an array comparative genomic hybridization test gave information of loss of heterozygosity. This helped to narrow the list of plausible diagnoses and eventually led to the diagnosis of pontocerebellar hypoplasia type I.