Inflammatory and infectious upper respiratory diseases (IURDs; ICD-10: J30-J39), such as diseases of sinonasal tract, pharynx and larynx, are growing health problems yet their genomic similarity is not known. We analyzed genome-wide association to eight IURDs (61,195 cases) among 260,405 FinnGen participants, meta-analyzing diseases in four groups based on an underlying genetic correlation structure. We aimed to understand which genetic loci contribute to susceptibility to IURDs in general and its subtypes. We detected 59 independent genome-wide significant (GWS) loci, distinguishing impact on sinonasal or pharyngeal diseases, or both. Fine-mapping implicated non-synonymous variants in 16 genes, including 10 linked to immune-related diseases. Phenome-wide analysis implicated asthma and atopic dermatitis at sinonasal disease loci and inflammatory bowel diseases, and other immune-mediated disorders at pharyngeal disease loci. IURDs also genetically correlated with autoimmune diseases such as rheumatoid arthritis, autoimmune hypothyroidism, and psoriasis. Finally, we associated separate gene pathways in sinonasal and pharyngeal diseases that both contribute to type 2 immunological reaction. We show shared heritability among IURDs that extends to several immune-mediated diseases with diverse mechanisms, such as type 2 high inflammation.