At least three different sizes of GH-1 gene deletions (approximately 6.7, 7.0 and 7.6 kilobases) have been detected by Southern blot analysis of DNA from individuals with familial isolated GH deficiency type IA (IGHD1A). It is likely that these deletions result from unequal crossing over events between homologous regions that flank the GH-1 gene. Heterogeneity in clinical phenotypes is suggested by reports of good responses to exogenous GH treatment in most IGHD1A subjects with 7.6 kilobase deletions as opposed to poor responses in many subjects with smaller deletions. To determine if characteristic differences in gene deletions could be detected that correlate with response to treatment we analyzed the DNA sequences that normally flank the GH-1 gene. Digestion patterns of the PCR amplification products of these sequences from DNA of IGHD type IA patients with the restriction endonucleases BglI, HaeII, or SmaI showed characteristic differences for each of the three deletion sizes studied. The location and size of all deletions agreed with previous size estimates based on Southern blot analysis. Interestingly, clinical differences observed in the development of high titers of anti-GH antibodies and poor growth responses after GH treatment are unexplained, since discordant outcomes were observed in patients who had deletions of the same size and approximate location.