Human GH is encoded by the GH-1 gene which belongs to the GH gene cluster encompassing a distance of about 65 kb on the long arm of chromosome 17. Familial isolated growth hormone deficiency (IGHD) is associated with at least four Mendelian disorders. These include two forms that have autosomal recessive inheritance (IGHD types IA and IB) as well as autosomal dominant (IGHD type II) and X-linked (IGHD III) forms. The aim of our study was to evaluate the prevalence of all GH-1 gene alterations by sequencing the whole GH-1 gene after PCR amplification among 151 affected subjects from 83 families with severe IGHD (height: <-4.5 SD score). A high frequency of GH-1 gene alterations was found in families with IGHD type IA (8/12, 66.7%), whereas only a low frequency of GH-1 gene defects was present in all the other GH-deficient families (7/71, 9.9%). The absolute frequency of GH-1 gene deletions was 8.7% (6/69), 11.8% (4/34), and 18.7% (9/48) in Northern Europeans, Mediterraneans, and Asians, respectively, giving an overall frequency of 12.5% (19/151). The sizes of the deletions were heterogeneous with the most frequent (78%) being 6.7 kb. In addition, 6% (9/151) of the patients presented GH-1 gene mutations such as frameshift, stop codon and splicing error. Furthermore, total GH-1 gene abnormalities varied among different populations from 11.6% in Northern Europe, 14.7% in Mediterranean countries and 31.2% in Asia. Most striking, however, was the low frequency rate of 1.7% (2/119) of GH-1 gene mutations responsible for the most common phenotype of IGHD, namely type IB, among the subjects characterized by the production of deficient but detectable amounts of GH after provocative stimuli. This finding underlines the necessity to focus rather on the promoter region of the GH-1 gene (cis-acting elements and trans-acting factors), and on other candidate genes specific for the GH axis than the GH-1 gene itself to define genetically the IGHD type IB phenotype in more detail.