Objective: To investigate the correlation between various co-morbidities of COVID-19 patients with persistent PCR positivity in hospitalized patients. Study Design: Prospective Observational. Setting: Nishtar Medical University, Multan COVID Isolation Wards, and ICU. Period: September 15 to September 14, 2020. Material & Methods: The study sample included 162 hospitalized patients who underwent COVID-19 PCR testing at admission, 4 weeks, and 8 weeks, and their comorbidities data were collected. Multiple regression analysis was performed to determine the relationship between co-morbidities and COVID-19 PCR positivity. Results: Among 162 patients, seventy-nine (48.8%) were male and the mean age of the patients was 53.46±15.81 years. Out of 162 patients, 70 (43.2%) tested positive for COVID-19, while 92 (56.8%) tested negative. Among 70 patients who had positive PCR, 45(64.28%) patients had prolonged positive PCR (at 4 weeks) and out of 45, 29 (64.45%) again remained positive at 8 weeks. While carrying out the multiple linear regression, the results indicated that the presence of hypertension, diabetes, and lung disease was positively associated with persistent COVID-19 PCR positivity (at 4 and 8 weeks). However, no significant association was found between persistent COVID-19 PCR positivity and liver disease, malignancy, and ischemic heart disease. Conclusion: The study highlights the importance of considering co-morbidities like diabetes, hypertension, and lung disease, in predicting persistent COVID-19 PCR positivity in hospitalized patients. Further research is needed to confirm these findings and investigate the underlying mechanisms of these associations.