Introduction: Studies have demonstrated the effectiveness of Prone lying for minimum of 6 hours improves the oxygen saturation of the COVID subjects. But, very few studies have demonstrated he occurring musculoskeletal dysfunctions in subjects with COVID who are admitted in COVID-ICU with regular Physiotherapy following CARP protocol and medical care. Objective: The study intend to investigate the type, mechanism and pathogenesis of the musculoskeletal dysfunctions which have occurred in the subjects with COVID. Methods: This was an analytical type of study conducted on 300 COVID positive subjects who were recruited after 7th day of admission in Krishna Hospital, and were divided into two groups. Group A with 3 hour prone lying and Group B with 6 hours prone lying depending on the Physiotherapy intervention given. Structured Orthopedic Manual Therapy Assessment Format was used to analyze the subjects among both the groups for any Musculoskeletal dysfunction they currently posses. Results: The results of the study showed definite and significant difference in the occurrence of Musculoskeletal dysfunctions in both the groups of 3 hours and 6 hours with outcome measure Structured Orthopedic Manual Therapy Assessment Format; subparameters: pain, tender point and accessory glide: showed the more significant presence in group B (6 Hours) and between-group difference existed with p-value: 0.05. In sub-parameters like: type of pain, Combined movement pattern, Janda__ampersandsignrsquo;s movement pattern, spasm, fascia and muscle mobility and neural tension testing p-value showed: 0.005 and 0.05, 0.05 and 0.05, 0.112 and 0.05, 0.112 and 0.05, 0.05 and 0.05, 0.891 and 0.715 (for ULTT) and 0.815 and 0.521 for LLTT respectively. Conclusion: Six hours of prone lying in subjects infected with Coronavirus have good outcome concerning Respiratory as well as Cardiac parameters, but, in the present study Group A showed very less amount of Musculoskeletal dysfunction occurrence when compared to Group B. But, further studies are needed to determine whether 3 hours of prone lying if given twice a day, can have any affect on musculoskeletal dysfunction in such subjects.