This study characterized heterozygosity-rich regions (HRR) in 30 Italian and 19 worldwide goat breeds using the Illumina GoatSNP50k BeadChip. The aim was to explore inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic analysis revealed a clear separation between non-European and European breeds, with a north-south geographic cline within Europe. High correlation coefficients (over 0.9) were found between descriptive HRR parameters obtained with SW and CR methods. A total of 166 HRR islands were detected, with CHI1, CHI11, CHI12, and CHI18 harboring the highest number. Genes in these regions were linked to factors such as productivity, reproduction, immunity, and environmental adaptation. The Montecristo feral goat showed the highest number of HRR islands despite high inbreeding, suggesting balancing selection events. HRR may harbor loci related to key functional traits and avoid harmful homozygous genotypes. The study highlights the importance of HRR in understanding genomic diversity and adaptation in goats, particularly in relation to anthropogenic selection and environmental interaction. The results suggest that HRR patterns are species-specific and may provide insights into the mechanisms regulating genome modeling. The study also identified several HRR islands associated with genes involved in immune response, reproduction, and environmental adaptation. The Montecristo goat, despite high inbreeding, showed the highest number of HRR islands, indicating potential balancing selection. The study underscores the importance of HRR in understanding genetic diversity and adaptation in goats, and the need for further research to refine HRR detection methods and parameters. The findings contribute to the understanding of genetic diversity and adaptation in goats, with implications for breeding and conservation strategies.This study characterized heterozygosity-rich regions (HRR) in 30 Italian and 19 worldwide goat breeds using the Illumina GoatSNP50k BeadChip. The aim was to explore inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic analysis revealed a clear separation between non-European and European breeds, with a north-south geographic cline within Europe. High correlation coefficients (over 0.9) were found between descriptive HRR parameters obtained with SW and CR methods. A total of 166 HRR islands were detected, with CHI1, CHI11, CHI12, and CHI18 harboring the highest number. Genes in these regions were linked to factors such as productivity, reproduction, immunity, and environmental adaptation. The Montecristo feral goat showed the highest number of HRR islands despite high inbreeding, suggesting balancing selection events. HRR may harbor loci related to key functional traits and avoid harmful homozygous genotypes. The study highlights the importance of HRR in understanding genomic diversity and adaptation in goats, particularly in relation to anthropogenic selection and environmental interaction. The results suggest that HRR patterns are species-specific and may provide insights into the mechanisms regulating genome modeling. The study also identified several HRR islands associated with genes involved in immune response, reproduction, and environmental adaptation. The Montecristo goat, despite high inbreeding, showed the highest number of HRR islands, indicating potential balancing selection. The study underscores the importance of HRR in understanding genetic diversity and adaptation in goats, and the need for further research to refine HRR detection methods and parameters. The findings contribute to the understanding of genetic diversity and adaptation in goats, with implications for breeding and conservation strategies.