Goats play a crucial role in providing humans with various types of valuable products including milk and meat. The underlying genetic mechanisms of important morphological aspects remain largely unknown in goats, highlighting the need for further investigation. A genome-wide association analysis (GWAS) was conducted for three morphological phenotypes in Egyptian goats. All animals were genotyped using the Illumina 65 K SNP BeadChips. Results of GWAS for wattles identified two significant (P ≤ 1.4 × 10^–6, false discovery rate (FDR) ≤ 0.05) single nucleotide polymorphisms (SNPs) on chromosome 10 within a region (72–74 Mb) containing FMN1 and GREM1 genes that are important for limb development and growth. For horns, three significant SNPs were identified on chromosome 1 (119–131 Mb) harbouring candidate genes for embryonic development and tissue differentiation, such as CEP70, DZIP1L, CLDN18, SOX14, and SLC35G2. For supernumerary teats, four significant SNPs located on chromosomes 25 (8.7 Mb), 9 (47.8 Mb), 17 (45.1 Mb), and 28 (6.7 Mb) were identified, harbouring candidate genes involved in morphogenesis and reproductive traits such as EMP2, MDN1, PCDH10, and GHITM. This study identified novel candidate genes alongside previously reported ones in other goat breeds, suggesting their potential as candidate genes for the studied traits in Egyptian goats.