This study was performed with the aim of determining the diagnostic profile of newborns with hypotonia and of analyzing the usefulness of different procedures in the diagnostic process. One hundred thirty-eight hypotonic newborns were identified through the search of hospital records in a 10-year period: 121 (88%) had central hypotonia and 13 (9%) had peripheral hypotonia, whereas 4 (3%) remained unclassified. Analysis of the contribution of clinical data and results of investigations led to the construction of an algorithm, by which all cases in the group were diagnosed. Step 1, which included clinical data and results of examinations, solved 50% of all diagnosed cases. Neuroimaging techniques made up step 2 and contributed to the diagnosis in 13%. Step 3 was accomplished by a search through Oxford Medical Databases, which yielded the final diagnosis in 9%, whereas karyotyping and fluorescent in situ hybridization for Prader-Willi syndrome comprised step 4 and contributed to the diagnosis in 6.5%. Biochemical tests formed step 5 and contributed to the diagnosis in 6%. Step 6, which included specific investigations of muscle and nerve, was diagnostic in 6%. The remaining cases (6.5%) were diagnosed only after several follow-up examinations. These results could assist the neonatologist when deciding the diagnostic approach to floppy newborns.