ABSTRACT Background Health assessment questionnaire (HAQ) is increasingly being used for assessing health outcome in the Rheumatoid Arthritis (RA) patients. The present study aims to determine the relationship between the functional status and disease activity of South Indian patients with RA at initial presentation using HAQ and tools such as disease activity score (DAS -28 ESR) and Clinical Disease Activity Index (CDAI). Methods This was a cross sectional observational study on relationship between DAS-28 ESR, CDAI and HAQ tools in 100 consecutive newly diagnosed patients with RA in Southern India. Patients were stratified based on HAQ score and their association was studied using chi square test and Mann Whitney U test. Results The patients were classified as Group I with HAQ score <1 (n=73) and Group II with HAQ score>1 (n=27). The median TJC (22 vs 12; p<0.01) and SJC (7 vs 5; p=0.04) scores were significantly higher in patients with HAQ>1 group. Also, patients in HAQ>1 group had significantly higher median DAS-28 ESR (7.5 vs 6.5; p<0.01) and CDAI (43 vs 29.5; p<0.01). Conclusion There was a very high positive correlation between HAQ with DAS 28 ESR and CDAI score at initial presentation in RA patients. Hence HAQ score can be used earlier in the disease course to assess functional limitations and monitor disease activity in RA patients.