Purpose (1) To determine the prevalence of musculoskeletal complaints (MSCs) in the non-affected bodily structures in individuals with brachial plexus injury (BPI) and (2) to analyse factors associated with MSCs and disability. Methods Survey among individuals with BPI and a control group. Multivariable logistic and linear regression analyses were used to identify factors associated with MSCs or disability. Results Forty-nine percent of individuals (34/70) with BPI experienced MSC, which was not significantly different from controls (35%, n = 40/113). Complaints were most often located in high back (OR = 3.6) or non-affected limb (OR = 2.2) or neck (OR = 2.1). Greater disability was associated with the presence of MSC in individuals with BPI (OR = 1.1, 95% confidence interval (95% CI) = 1.0; 1.1). Those with no or a low level of education (B = -10.2, 95% CI = -19.6; -1.4), a history of nerve surgery (B = 11.1, 95% CI = -0.2; 20.9), and moderately affected active range of motion (AROM) of the affected limb (B = 20.7, 95% CI = 8.8; 31.0) experienced most disability. Individuals with severely affected AROM showed a wide range of experienced disability. Conclusions Clinicians should be aware that almost half of individuals with BPI have MSCs in the non-affected bodily structures, which was associated with increased disability.