Background <p>Rheumatoid Arthritis (RA) is a prevalent autoimmune disease affecting approximately 84,338 individuals in Egypt. Genetic predispositions, such as the PTPN22 and PADI4 genes, are linked to RA risk. PTPN22, a protein tyrosine phosphatase, a regulator of T-cell receptor signalling and PADI4, which is involved in citrullination, have shown varying levels of association with RA across populations. Studies have been inconclusive regarding their roles in RA susceptibility, progression, and activity.</p> Patients and methods <p>A total of 240 participants were included in this study, RA patients and healthy controls from Aswan, Egypt. Genomic analysis was conducted to evaluate PTPN22 and PADI4 polymorphisms and their associations with RF and ACPA, Also, their correlation with disease activity markers, such as ESR, CRP, PGA and the Disease Activity Score (DAS28).</p> Results <p>No significant association between PTPN22 and RA with p value ≥ 0.05 with good matching regarding age and sex. However, PTPN22 significantly correlated with RF and ACPA, with p-value of 0.006 and &lt; 0.001, respectively, suggesting its diagnostic value in RA. No significant associations were found between PTPN22 and disease activity markers such as the ESR and CRP. In contrast, PADI4 levels were elevated in the control groups with p value &lt; 0.001 which is against the study hypothesis, which conflicts with findings from other studies. Despite this, PADI4 demonstrated greater specificity (73.3%), in RA diagnosis than did PTPN22 (45.3%), making it a potential diagnostic marker in combination with RF and ACPA.</p> Conclusion <p>Our study revealed no significant associations between PTPN22 or PADI4 polymorphisms and RA susceptibility in the Aswan population. However, both genes were correlated with diagnostic markers such as RF and ACPA. The PADI4 has potential as a diagnostic marker with high specificity.</p>